Re: [gmx-users] (no subject)

[Tasneem Kausar]

Please specify your gromacs version.

On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua 
wrote:

> hi
> I am facing problem during hydrogen bond correlation c(t) with error
> segmentation fault
> I have used following flag for generate xtc file::- gmx trjconv -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> cluster
> then for hydrogen bond correlation used following flag ::-gmx hbond -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> following error I am getting
> Doing autocorrelation according to the theory of Luzar and Chandler.
> Segmentation fault (core dumped)
> please suggest me to solve this problem
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Re: [gmx-users] CA ions

[Tasneem Kausar]

You are going to the right way. There are more options given in gmx genion.
Check -pname and -nname. These options will help you to select the name of
positive and negative ions.


On Sat, 7 Dec 2019, 5:05 am Iman Katouzian,  wrote:

> Good day,
>
> I want to simulate my protein in gromacs and in this simulation I need to
> add a certain concentration of CA ions to my system. However, I have no
> idea about how to do this so first I have to neutralize my system and then
> need to add the needed CA ions which act as binding agents* (necessary
> factor in experiments) *in my protein. I have heard that with -neutral and
> -conc for adding the certain concentration I can do this thing.
> I would appreciate it if somebody can help me with this issue.
>
> Thanks.
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
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Re: [gmx-users] SASA calculation for one replica in REMD

[Tasneem Kausar]

Check gmx sasa -h
It is implemented in Gromacs

On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs Users,
>
> I did replica exchange molecular dynamics simulation which contains 25
> replicas. Now I want to calculate the solvent accessible surface area of
> the surfactant (the first replica in my REMD) I used in my simulation at
> 298 K. How can I do that?
>
> Can anyone help me?
>
> Thank you.
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Re: [gmx-users] calculating energy between certain groups

[Tasneem Kausar]

First of all define energy groups in mdp file. Then run gmx grompp with
that mdp to generate a new tpr. In gmx mdrun provide reference file (eg
tpr).


On Mon, May 21, 2018 at 7:19 AM, Irem Altan  wrote:

> I tried the following:
>
> mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0
>
> and also I can verify from the output file that it didn’t use GPUs.
> However, I still get the same error with gmx enemat:
>
> GROMACS:  gmx enemat, version 2016.3
> Executable:   /opt/gromacs/bin/gmx_mpi
> Data prefix:  /opt/gromacs
> Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
> Command line:
>   gmx_mpi enemat -f umbrella0.edr
>
> Opened umbrella0.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in
> energy file
> WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
> WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
> WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
> WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file
>
> Will select half-matrix of energies with 0 elements
> Last energy frame read 2000 time 2.000
> Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
> Segmentation fault
>
> What could be the problem?
>
> Best,
> Irem
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Re: [gmx-users] Fwd: how to get .mdp files

[Tasneem Kausar]

mdp file is parameter file for md simulations.
You need to copy if you want to use the parameters used in the tutorial.
You can also change that parameter according to your use and need.

On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa  wrote:

> -- Forwarded message --
> From: "neelam wafa" 
> Date: 17 Feb 2018 00:57
> Subject: how to get .mdp files
> To: 
> Cc:
>
> Hi
> I am new to this list. I have run the gromacs tutorial ' lysosime in
> water'. now i have to run a protein ligand simmulation. But i am confused
> about how to generate .mdp files as in tutorial they have used five .mdp
> files which are to be downloaded from bevanlab.biochem. These are ions.mdp,
> em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these
> have to be generated with aome software according to the protein and
> ligand.
>
> Thanks in advance.
>
> Regards
> Neelam
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Re: [gmx-users] pH dependent simulation

[Tasneem Kausar]

Thanks for correcting..

On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/27/17 1:02 AM, Tasneem Kausar wrote:
>
>> pKa of amino acid residue is a constant quantity. Depending on the pH you
>>
>
> That's not strictly true. Titratable amino acids can be found in unique
> microenvironments that cause shifts in canonical values. For instance,
> there are some catalytic lysines known in hydrophobic environments that
> have pKa values of ~4 instead of the canonical value of ~10.5.
>
> -Justin
>
> can protonate and deprotonate amino acid according to the pKa of particular
>> residue.
>>
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>> On Mon, Nov 27, 2017 at 9:39 AM, <za...@tezu.ernet.in> wrote:
>>
>> Hello Everyone
>>>
>>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>>> positively charged residues.
>>>
>>> However upon predicting the pKa values using H++ server, I am getting the
>>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And
>>> the
>>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>>> should have different pKa values at pH 7 and 9).
>>>
>>> Whether I am in the right direction or doing something wrong!!!
>>>
>>> Can anyone kindly suggest me how to proceed further?
>>>
>>> Any suggestion is appreciated.
>>>
>>> Thank You
>>> Zaved
>>>
>>>
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>>>
> --
> ==
>
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> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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>
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>
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Re: [gmx-users] pH dependent simulation

[Tasneem Kausar]

pKa of amino acid residue is a constant quantity. Depending on the pH you
can protonate and deprotonate amino acid according to the pKa of particular
residue.


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On Mon, Nov 27, 2017 at 9:39 AM,  wrote:

> Hello Everyone
>
> I am trying to simulate a protein at two pH (7.4 and 9.0) using
> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
> positively charged residues.
>
> However upon predicting the pKa values using H++ server, I am getting the
> same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
> should have different pKa values at pH 7 and 9).
>
> Whether I am in the right direction or doing something wrong!!!
>
> Can anyone kindly suggest me how to proceed further?
>
> Any suggestion is appreciated.
>
> Thank You
> Zaved
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
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Re: [gmx-users] .coordinate(gro) file

[Tasneem Kausar]

Fitsiou already suggested you to change the number of atoms at top  second
line of the gro file.

On Mon, Nov 6, 2017 at 10:22 AM, rose rahmani  wrote:

> Hi dear
>
> yes,i did
>
> On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni  >
> wrote:
>
> > Hi, did you change the total number of atoms in your file ?
> > (the second line at the top of the gro file?)
> >
> > Best, Eleni
> > > On 5 Nov 2017, at 20:33, rose rahmani  wrote:
> > >
> > > Hi
> > >
> > > I have structure.gro file
> > >
> > > 32
> > > .
> > > .
> > > .
> > >
> > >   0ZnSS29   29   0.000   0.191   2.029
> > >0ZnSS30   30   0.000   0.574   2.029
> > >0ZnS   Zn31   31   0.000   0.000   2.164
> > >0ZnS   Zn32   32   0.000   0.383   2.164
> > >   0.0   0.0   0.0
> > >
> > > and AA.gro
> > >
> > > PRODRG COORDS
> > >   12
> > >1PDB  O1   0.147   2.267   0.468
> > >1PDB  C2   0.182   2.373   0.415
> > >1PDB  OC   3   0.151   2.486   0.453
> > >1PDB  CA   4   0.318   2.368   0.351
> > >1PDB  N5   0.390   2.383   0.475
> > >1PDB  H2   6   0.368   2.471   0.516
> > >1PDB  H3   7   0.488   2.379   0.457
> > >1PDB  H1   8   0.364   2.309   0.538
> > >1PDB  CB   9   0.343   2.234   0.282
> > >1PDB  CG2 10   0.255   2.218   0.157
> > >1PDB  OG1 11   0.480   2.228   0.243
> > >1PDB  HG1 12   0.499   2.141   0.197
> > >   0.53100   0.53100   0.53100
> > > and i want to make one coordinate file for both of them(like
> > > protein-ligand tutorial)
> > >
> > > but when i copy structure.gro to the end of AA.gro to
> > make>>>complex.gro, i
> > > cant check it in any viewer like VMD,it seeems that complex.gro is not
> > > correctly modified,could you please tell me what is wrong?!
> > >
> > > Thank you
> > > --
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Re: [gmx-users] pdb (CTAB) into .GRO

[Tasneem Kausar]

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In
your pdb file residue name XXX is not defined in gromos ff. If your system
is other than protein then use ATB to generate topolgy.


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On Fri, Nov 3, 2017 at 2:19 PM, Adriano Santana Sanchez <
adriano.santanasanc...@kaust.edu.sa> wrote:

>  Dear all,
>
>  I am a beginner with gromacs and I have already done some online
> tutorials.
>  I am now trying to create from a PDB coordinate file (a CTAB molecule) the
>  corresponding .GRO and .TOP files to run MD simulations.
>
>  gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
>
>  then choose FF gromos96 53a6 but get error message:
>
>  Residue 'XXX' not found in topology database
>
> I am sure this FF has been used for this molecule before and I cannot
>
> find this CTAB on the residue database. What can I do?
>
> Thanks,
> Adriano
>
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Re: [gmx-users] itp file for aminoacids

[Tasneem Kausar]

You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs does
the job of making itp.


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On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani  wrote:

> hello
>
> how can i make an .itp file for amino acids?
> which amino acids is identified in AMBER forcefield?
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Re: [gmx-users] MD simulation error : rRNA simulaion

[Tasneem Kausar]

In energy group you have given Potein and non-Protein and you are not
simulation a protein but RNA.

On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya 
wrote:

> Dear gromacs,
> Greetings
> I am trying to run a NVT with the following command.
>
> My mdp file is below
>
> title   = Protein-ligand complex NVT equilibration
> define  = -DPOSRES  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 500   ; save coordinates every 0.2 ps
> nstvout = 500   ; save velocities every 0.2 ps
> nstenergy   = 500   ; save energies every 0.2 ps
> nstlog  = 500   ; update log file every 0.2 ps
> energygrps  = Protein Non-protein
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10 ; 10 fs
> *rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)*
> *rvdw= 1.4   ; short-range van der Waals cutoff (in nm)*
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc_grps = Protein Non-Protein; two coupling groups - more accurate
> tau_t   = 0.1   0.1 ; time constant, in ps
> ref_t   = 300   300 ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl  = no; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
>
>
> Error :
>
> GROMACS:  gmx grompp, VERSION 5.1.4
> Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
> Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
> Command line:
>   gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
> index.ndx
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#
>
> *ERROR 1 [file nvt.mdp]:*
> *  With Verlet lists rcoulomb!=rvdw is not supported*
>
> Setting the LD random seed to 2859163501
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Setting gen_seed to 1604041440
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
>
>
> When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
> different error
> like
> "Fatal error:
> Group Protein referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp."
>
>
> Please help me to solve the problem.
> Thanks
> --
> *Hemant Arya*
> Research Scholar
> UGC-RGNF
> Centre for Bioinformatics,
> School of Life Sciences,
> Pondicherry University
> Kalapet
> Puducherry- 605014
> INDIA
> Contact No. +91 9597221248
>+91 2930-244141
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Re: [gmx-users] checking simulation progress

[Tasneem Kausar]

see gmx check -h option

On 3 Oct 2017 21:33, "Bukunmi Akinwunmi"  wrote:

> dear gmx-users,
> my simulation has been running for sometime but now I want to know how
> long is left for the simulation to be completed. I need help with the
> command to analyse a running simulation.
>
> Best regards,
> Bukunmi
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Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Thank You

On Fri, Sep 22, 2017 at 1:35 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dear Tsaneem,
>
> Negative values don’t signify lack of correlation, but anticorrelation.
> Also, by omitting negative values you introduce a slight bias in your fit
> towards longer half-life.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 22 Sep 2017, at 06:18, Tasneem Kausar <tasneemkausa...@gmail.com<
> mailto:tasneemkausa...@gmail.com>> wrote:
>
> Thank you for reply
>
> I read the references and I know that one of the columns of g_hbond output
> is without subtraction
> and the value ranges between 0 to 1. The only help I need is that can I
> fit the curve of the first column (which has negative value) and neglect
> the range of curve of negative part while fitting to get the exponential
> parameters of the curve. This seems to me reasonable only for getting
> information parameter as negative ACF value mean no correlation parameter.
>
> Any help will be appreciated.
>
> Thanks in Advance.
>
> On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund <erik.markl...@kemi.uu.se<
> mailto:erik.markl...@kemi.uu.se>>
> wrote:
>
> Dear Tasneem,
>
> Quite often ACF calculations involve subtraction of the average signal,
> and this normally renders some negative values in the ACF. It’s been a bit
> too long since I dealt with the gmx hbond code, but I suspect that is what
> is going on here. I suggest reading the references that gmx hbond mentions,
> where the four quantities in the output are defined.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> erik.markl...@kemi.uu.se>
>
> On 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausa...@gmail.com<
> mailto:tasneemkausa...@gmail.com><
> mailto:tasneemkausa...@gmail.com>> wrote:
>
> Still waiting for suggestions.
>
> On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausa...@gmail.com
> <mailto:tasneemkausa...@gmail.com>
> <mailto:tasneemkausa...@gmail.com>>
> wrote:
>
> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
> I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Thank you for reply

I read the references and I know that one of the columns of g_hbond output
is without subtraction
 and the value ranges between 0 to 1. The only help I need is that can I
fit the curve of the first column (which has negative value) and neglect
the range of curve of negative part while fitting to get the exponential
parameters of the curve. This seems to me reasonable only for getting
information parameter as negative ACF value mean no correlation parameter.

Any help will be appreciated.

Thanks in Advance.

On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dear Tasneem,
>
> Quite often ACF calculations involve subtraction of the average signal,
> and this normally renders some negative values in the ACF. It’s been a bit
> too long since I dealt with the gmx hbond code, but I suspect that is what
> is going on here. I suggest reading the references that gmx hbond mentions,
> where the four quantities in the output are defined.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausa...@gmail.com<
> mailto:tasneemkausa...@gmail.com>> wrote:
>
> Still waiting for suggestions.
>
> On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausa...@gmail.com
> <mailto:tasneemkausa...@gmail.com>>
> wrote:
>
> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
> I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
>  I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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[gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
 I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar
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Re: [gmx-users] ERROR IN EXECUTION ---GMX

[Tasneem Kausar]

If you are using linux and gromacs is installed in /user/local/bin check
these steps

vi ~/.bashrc
in the last line of the file add
source /usr/local/bin/GMXRC

and save this.






On Mon, Aug 28, 2017 at 12:08 PM, Neha Gupta 
wrote:

> Hi,
>
> I gave these commands initially
>
> PATH=$PATH:"/usr/local/gromacs/bin/"  (this mentions path to gmx)
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"
>
> For that, I got the response,
>
> gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> I went through "lib" folder (had mentioned its contents above)  and lib64
> which contains libgromacs.so.0.0.0
>
>
> Thanks,
> Neha
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Re: [gmx-users] gmx distance

[Tasneem Kausar]

Ctrl+D

On Fri, Aug 25, 2017 at 5:06 PM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hello, I am trying to find the average distance between two groups in a
> trajectory, defined by the index.ndx file and the traj.xtc,
>
> the options are
>
>
> Available static index groups:
> Group 0 "System" (1 atoms)
> Group 1 "DNA" (1333 atoms)
> Group 2 "NA" (71 atoms)
> Group 3 "CL" (31 atoms)
> Group 4 "DEHP" (66 atoms)
> Group 5 "Ion" (102 atoms)
> Group 6 "NA" (71 atoms)
> Group 7 "CL" (31 atoms)
> Group 8 "DEHP" (66 atoms)
> Group 9 "Other" (66 atoms)
> Group 10 "NA" (71 atoms)
> Group 11 "CL" (31 atoms)
> Group 12 "DEHP" (66 atoms)
> Group 13 "Water" (31830 atoms)
> Group 14 "SOL" (31830 atoms)
> Group 15 "non-Water" (1501 atoms)
> Group 16 "Water_and_ions" (31932 atoms)
> Group 17 "DEHP" (66 atoms)
> Group 18 "DNA" (1333 atoms)
> Specify any number of selections for option 'select'
> (Position pairs to calculate distances for):
> (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > 1
> Selection '1' parsed
> > 4
> Selection '4' parsed
> >
>
>
> however, then, which command to issue to start the distance generation?
>
> Thanks
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
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> http://www.phap.no/ | FAP ]
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Re: [gmx-users] problem in extending a simulation run

[Tasneem Kausar]

As error says you have run previous simulation on gromacs-5.0.2 and now you
are running with gromacs 5.0.6

On 18 Aug 2017 12:11, "manindersingh rajawat" <
rajawat.manindersi...@gmail.com> wrote:

> Dear all,
>
> I want extend a 100ns run to 150 ns. For this I use following commands:
>
> gmx convert-tpr -s md_100ns.tpr -extend 5 -o md_150ns.tpr
>
> gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb
>
> But mdrun taken it as a new run and began a full 150ns run:
> starting mdrun 'Protein in water'
> 7500 steps, 15.0 ps
>
> so i stopped it, and run with checkpoint input as following:
>
> gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
>
> Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>
>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
> Using 1 MPI thread
> Using 4 OpenMP threads
> Compiled SIMD instructions: SSE2 (Gromacs could use AVX2_256 on this
> machine, which is better)
>
> WARNING: This run will generate roughly 19040 Mb of data
>
> starting mdrun 'Protein in water'
> 7500 steps, 15.0 ps (continuing from step 5000, 10.0 ps).
> step 5600
>
> It starts well from the checkpoint, but due to little confusion i stopped
> it. and ran the following command:
>
> gmx mdrun -v -s md_150ns.tpr -cpi state_prev.cpt -c md_150ns.pdb
>
> It gives the following error
>
> Reading file md_150ns.tpr, VERSION 5.0.6 (single precision)
> Changing nstlist from 5 to 40, rlist from 1.2 to 1.223
>
>
> Reading checkpoint file state_prev.cpt generated: Fri Mar 24 05:36:56 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>
>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx, VERSION 5.0.6
> Source code file:
> /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
> 2204
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> When i run the previous command, that is
>
> gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
>
> It starts giving the same error to this also.
>
> Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>
>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx, VERSION 5.0.6
> Source code file:
> /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
> 2204
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Please help me to resolve it.
>
> Thanks
> --
> Maninder Singh
> Research Fellow,
> LSN-104, Computational Biology and Bioinformatics Unit,
> Molecular and Structural Biology Division,
> CSIR-Central Drug Research Institute,
> Sector-10, Janakipuram Extension,
> Sitapur road,
> Lucknow
> India-226031
> M: +919129206276
> Email: rajawat.manindersi...@gmail.com
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> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read 

Re: [gmx-users] (no subject)

[Tasneem Kausar]

Number of hydrogen bond depends on the nature of your drug. It can be zero,
one or many.

On Thu, Aug 10, 2017 at 10:33 AM, saranya  wrote:

> Hi,
> I have done protein-drug simulations for 100ns. While calculating the
> hydrogen bond between the protein-drug complex I am getting only 2 hydrogen
> bonds.
> I just want to clarify that 2 hydrogen bonds mean very low, is it
> acceptable to get this minimum number of bond formation for the protein
> drug interaction?
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
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Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

[Tasneem Kausar]

Try this
1 | 13 & a N
This will select the group 1 and 13 and all the atom having atom ID N.

On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N 
wrote:

> Hello,
> I am having problems during creating the indexes for atoms which have same
> atom labelling for the two/three different molecules in the system (say
> nitrogen atom that is labelled as N in both the molecules).
>  whn i gave the command:-
> gmx make_ndx -f md.gro -o a.ndx
> i am getting the prompt as :-
> Reading structure file
> Going to read 0 old index file(s)
> Analysing residue names:
> There are: 1Protein residues
> There are:10  Other residues
> There are:   200  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
>   0 System   :  750 atoms
>   1 Protein:10 atoms
>   2 Protein-H: 5 atoms
>   3 C-alpha  : 1 atoms
>   4 Backbone   : 3 atoms
>   5 MainChain  : 3 atoms
>   6 MainChain+Cb   : 3 atoms
>   7 MainChain+H : 6 atoms
>   8 SideChain  : 4 atoms
>   9 SideChain-H  : 2 atoms
>  10 Prot-Masses :10 atoms
>  11 non-Protein   :  890 atoms
>  12 Other:   140 atoms
>  13 TMAO  :   140 atoms
>  14 Water   :   600 atoms
>  15 SOL :   600 atoms
>  16 non-Water   :   374 atoms
>
> Here i need say the nitrogen present in protein (1 protein: 10 atoms) index
> and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx
> file.ie.,
> i need the nitrogen present in protein and nitrogen's present in tmao in
> the index file..
> How can i get this..?? wht will be the commands for this... i tried with
> various commands but in vain
>
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>  Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in=22>
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Re: [gmx-users] Fwd: Broken chain / fragmentation

[Tasneem Kausar]

Try -pbc whole

On 27 May 2017 18:09, "Biplab Ghosh"  wrote:

> Dear Gromacs users,
>
> My Gromacs simulation on a protein terminated without any error and major
> warning. However, when I see the conformations, I found them broken.
>
> For trajectory conversion, I have used the following commands:
>
> gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump -ur
> compact  -o protein-md-center.xtc
>
> gmx trjconv -s protein-md.tpr -f protein-md-center.xtc -fit rot+trans -o
> protein-md-center-fit.xtc
>
>
>
> I would appreciate any help in figuring out where I am going wrong.
>
> Thank you all
> Biplab.
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Re: [gmx-users] md continuation

[Tasneem Kausar]

You can directly extend time with gmx covert-tpr -s old.tpr -o new.tpr
-extend 2

On 18 May 2017 15:34, "Kashif"  wrote:

> It means I should conver my md.mdp file for 40 ns from 20 ns in the same
> folder and then run this command ...
>
> grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend
>
> after that this command...
>
> mdrun -deffnm md_0_1
>
> Please suggest the correct command if it is not correct.
>
> regards
>
> kashif
>
>
> On Wed, May 17, 2017 at 3:22 PM, Kashif 
> wrote:
>
> > I have already run my 20 ns md simulation of my protein. The log file is
> > showing completion of my 20 ns data. I have also done analysis by using
> > trjconv command and g_rms.
> > Now I want to increase my simulation at least for 20 ns more and make my
> > data of protein simulation for 40 ns. Kindly help for continuation of my
> > simulation. I have used this command but it did not help and shows error.
> > command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
> >
> > error:
> > NOTE: 23 % of the run time was spent communicating energies,
> >   you might want to use the -gcom option of mdrun
> >
> >  Core t (s)Wall t (s)(%)
> >Time:   25.0002.843 879.2
> >   (ns/day)(hour/ns)
> > Performance:0.061  394.912
> > Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
> >
> > regards
> > kashif
> >
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Re: [gmx-users] md continuation

[Tasneem Kausar]

see command gmx convert-tpr

On Wed, May 17, 2017 at 3:22 PM, Kashif  wrote:

> I have already run my 20 ns md simulation of my protein. The log file is
> showing completion of my 20 ns data. I have also done analysis by using
> trjconv command and g_rms.
> Now I want to increase my simulation at least for 20 ns more and make my
> data of protein simulation for 40 ns. Kindly help for continuation of my
> simulation. I have used this command but it did not help and shows error.
> command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
>
> error:
> NOTE: 23 % of the run time was spent communicating energies,
>   you might want to use the -gcom option of mdrun
>
>  Core t (s)Wall t (s)(%)
>Time:   25.0002.843 879.2
>   (ns/day)(hour/ns)
> Performance:0.061  394.912
> Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
>
> regards
> kashif
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Re: [gmx-users] pdb2gmx handle the dna structure containing potassium

[Tasneem Kausar]

Take a look at you pdb file. May be potassium atom is defined as HETATM in
pdb. amber99sb-ildn ff has K in its ions.itp file.

On Wed, May 10, 2017 at 1:46 PM, Changdong LIU  wrote:

> Dear GROMACS users,
>
>
>  I used pdb2gmx to generate topology file for the g_quadruplex DNA which
> constains 3 potassiums.
>
>
>  If the 3 potassiums were deleted ,the pdb2gma successfully generated the
> topology file for DNA.
>
>
> But failed when the 3 potassiums were added into the pdb file. The
> topol.top is like:
>
>
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_DNA_chain_C.itp"
> #include "topol_Ion_chain_D.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> ---
>
> [ molecules ]
> ; Compound#mols
> DNA_chain_C 1
> Ion_chain_D 1
>
>
> It seems that pdb2gmx could not recognize both dna and potassiums.
>
> As the potassium is necessary for the stability of the DNA g_quadruplex,
> would you please give any suggestions how to generated the topology file
> containing the ions?
>
> Thanks.
>
>
> Best
>
> Changdong
>
>
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[gmx-users] Water molecules present at the protein-protein interface.

[Tasneem Kausar]

Dear all

I want to figure out dynamics and interaction of water molecules present at
the protein-protein interface.

My system has around 4 water molecules and 450 amino acid residues.

How interface water molecules can be identified from the bulk of water.

Thanks in Advance
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[gmx-users] Hydration shell

[Tasneem Kausar]

Dear all

Is it possible in gromacs to write trajectory of a system that have
interface residues and water molecules of first hydration shell?

Thanks in Advance
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Re: [gmx-users] Using the md integrator for calculating free energy of solvation

[Tasneem Kausar]

In the last line of mdp file couple-lambda0 and couple-lambda1 have the
same vdwq variable. It indicates A and B state of system. So grompp is
complaining about the identical states.

You can also see the alchemistry.org for detail information about the free
energy calculations.

On Wed, May 3, 2017 at 2:14 AM, Dan Gil  wrote:

> Thank you Dr. Lemkul,
>
> Following your advice, I was able to calculate the solvation free energy of
> two molecules that I am interested in. The results, unfortunately, were not
> what I expected. I want to try an alternative method, that is, the
> alchemical thermodynamic integration method.
>
> If I understand this correctly, I should be able to calculate the free
> energy difference between two systems A and B as I change the topology of
> the molecule from A to B in small steps.
>
> I wasn't able to find a tutorial online, but I attempted to try the method
> and I obtained this error from grompp:
>
> WARNING 1 [file grompp.mdp, line 43]:
>   The lambda=0 and lambda=1 states for coupling are identical
>
> I was hoping if you could help me understand what I am missing in my
> topology or mdp file.
>
> Topology:
>  [ moleculetype ]
> HEPT 3
>
>  [ atoms ]
>  1   opls_135  1   HEPTCH3  1 -0.180 12.011
>  opls_9610.36012.011
>  2   opls_136  1   HEPTCH2  2 -0.120 12.011
>  opls_9620.24012.011
>  3   opls_136  1   HEPTCH2  3 -0.120 12.011
>  opls_9620.24012.011
>  4   opls_136  1   HEPTCH2  4 -0.120 12.011
>  opls_9620.24012.011
>  5   opls_136  1   HEPTCH2  5 -0.120 12.011
>  opls_9620.24012.011
>  6   opls_136  1   HEPTCH2  6 -0.120 12.011
>  opls_9620.24012.011
>  7   opls_135  1   HEPTCH3  7 -0.180 12.011
>  opls_9610.36012.011
>  8   opls_140  1   HEPT  H  1  0.060  1.008
>  opls_965   -0.12018.998
>  9   opls_140  1   HEPT  H  1  0.060  1.008
>  opls_965   -0.12018.998
> 10   opls_140  1   HEPT  H  1  0.060  1.008
>  opls_965   -0.12018.998
> 11   opls_140  1   HEPT  H  2  0.060  1.008
>  opls_965   -0.12018.998
> 12   opls_140  1   HEPT  H  2  0.060  1.008
>  opls_965   -0.12018.998
> 13   opls_140  1   HEPT  H  3  0.060  1.008
>  opls_965   -0.12018.998
> 14   opls_140  1   HEPT  H  3  0.060  1.008
>  opls_965   -0.12018.998
> 15   opls_140  1   HEPT  H  4  0.060  1.008
>  opls_965   -0.12018.998
> 16   opls_140  1   HEPT  H  4  0.060  1.008
>  opls_965   -0.12018.998
> 17   opls_140  1   HEPT  H  5  0.060  1.008
>  opls_965   -0.12018.998
> 18   opls_140  1   HEPT  H  5  0.060  1.008
>  opls_965   -0.12018.998
> 19   opls_140  1   HEPT  H  6  0.060  1.008
>  opls_965   -0.12018.998
> 20   opls_140  1   HEPT  H  6  0.060  1.008
>  opls_965   -0.12018.998
> 21   opls_140  1   HEPT  H  7  0.060  1.008
>  opls_965   -0.12018.998
> 22   opls_140  1   HEPT  H  7  0.060  1.008
>  opls_965   -0.12018.998
> 23   opls_140  1   HEPT  H  7  0.060  1.008
>  opls_965   -0.12018.998
> ... And so on with the bonds, pairs, angles, and dihedrals directive.
>
> MDP File:
>
> ;Integration Method and Parameters
> integrator   = md
> nsteps   = 1
> dt = 0.002
> nstenergy= 1000
> nstlog   = 5000
>
> ;Output Control
> nstxout = 0
> nstvout = 0
>
> ;Cutoff Schemes
> cutoff-scheme= group
> rlist= 1.0
> vdw-type = cut-off
> rvdw = 2.0
>
> ;Coulomb interactions
> coulombtype  = pme
> rcoulomb = 1.0
> fourierspacing   = 0.4
>
> ;Constraints
> constraints  = all-bonds
>
> ;Temperature coupling
> tcoupl   = v-rescale
> tc-grps  = system
> tau-t= 0.1
> ref-t= 300
>
> ;Pressure coupling
> pcoupl = parrinello-rahman
> ref-p = 1.01325
> compressibility = 4.5e-5
> tau-p = 5
>
> ;Free energy calculation
> free-energy  = yes
> init-lambda  = 0
> delta-lambda = 0.1
> couple-moltype   = HEPT
> couple-lambda0   = vdwq
> couple-lambda1   = vdwq
>
> On Mon, Apr 3, 2017 at 2:05 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 4/3/17 2:01 PM, Dan Gil wrote:
> >
> >> Thank you Dr. Lemkul,
> >>
> >> I am trying to run 

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

If you are taking confout.gro as your starting input file, it will have all
water and ions of the previous simulation.

On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> Create index group that have both protein and ACO. gmx make_ndx will serve
> this task.
> Then create a pdb file file from gmx trjconv
> Or you can choose system as output and delete ions and solvent from any
> editor.
>
>
>
> On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal <abhisek.m...@gmail.com>
> wrote:
>
>> Hello,
>>
>> Alright. I have tried this but I'm stuck in the following scenario.
>> I'm using trjconv for getting pdb file of the protein-ligand complex (used
>> for umbrella sampling).
>> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>>
>> This is giving me the following prompt:
>> Select group for output
>> Group 0 ( System) has 27051263 elements
>> Group 1 (Protein) has  1588 elements
>> Group 2 (  Protein-H) has  1245 elements
>> Group 3 (C-alpha) has   158 elements
>> Group 4 (   Backbone) has   474 elements
>> Group 5 (  MainChain) has   633 elements
>> Group 6 (   MainChain+Cb) has   784 elements
>> Group 7 (MainChain+H) has   785 elements
>> Group 8 (  SideChain) has   803 elements
>> Group 9 (SideChain-H) has   612 elements
>> Group10 (Prot-Masses) has  1588 elements
>> Group11 (non-Protein) has 27049675 elements
>> Group12 (  Other) has59 elements
>> Group13 (ACO) has59 elements
>> Group14 ( NA) has 16615 elements
>> Group15 ( CL) has 16615 elements
>> Group16 (  Water) has 27016386 elements
>> Group17 (SOL) has 27016386 elements
>> Group18 (  non-Water) has 34877 elements
>> Group19 (Ion) has 33230 elements
>> Group20 (ACO) has59 elements
>> Group21 ( NA) has 16615 elements
>> Group22 ( CL) has 16615 elements
>> Group23 ( Water_and_ions) has 27049616 elements
>> Group24 (
>>
>> Now how can I be able to get both Protein+ACO as a pdb file ?
>> If I could get Protein+ACO, then I could strip the box size for further
>> umbrella sampling procedure.
>>
>> However, is it possible to go with the following way:
>> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>>
>> Please suggest me a way.
>>
>> Thank you.
>>
>> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > Take a configuration of interest, strip the solvent, put it in a box you
>> > think is good, and re-equilibrate just like you did before you started.
>> >
>> > Mark
>> >
>> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal <abhisek.m...@gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Yes, I did when I started the simulation. The box size I used to start
>> > the
>> > > simulation was very big(I was dealing with an unknown sample). After
>> > > successfully generating the configurations I realized that further
>> work
>> > > could move faster if I could trim the box size little bit now.
>> > > So is there any way now to reduce the box size and proceed with
>> relevant
>> > > configurations towards PMF generation ?
>> > > Please suggest me a way here.
>> > >
>> > > Thank you.
>> > >
>> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" <mark.j.abra...@gmail.com>
>> > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > You get to choose the box size eg with editconf when you set up your
>> > > > simulation. It's not pre-defined ;-)
>> > > >
>> > > > Mark
>> > > >
>> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal <abhisek.m...@gmail.com>
>> > wrote:
>> > > >
>> > > > > Hello,
>> > > > >
>> > > > > Another thing I wanted to ask.
>> > > > > After generating configurations I found out that the predefined
>> box
>> > > size
>> > > > > (used to reach so far) is excessively high.
>> > > > > Is it possible to trim the box size to perform further mdrun
>> during

Re: [gmx-users] cant load trajectory, low memory

[Tasneem Kausar]

Create index group that have both protein and ACO. gmx make_ndx will serve
this task.
Then create a pdb file file from gmx trjconv
Or you can choose system as output and delete ions and solvent from any
editor.



On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal 
wrote:

> Hello,
>
> Alright. I have tried this but I'm stuck in the following scenario.
> I'm using trjconv for getting pdb file of the protein-ligand complex (used
> for umbrella sampling).
> trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr
>
> This is giving me the following prompt:
> Select group for output
> Group 0 ( System) has 27051263 elements
> Group 1 (Protein) has  1588 elements
> Group 2 (  Protein-H) has  1245 elements
> Group 3 (C-alpha) has   158 elements
> Group 4 (   Backbone) has   474 elements
> Group 5 (  MainChain) has   633 elements
> Group 6 (   MainChain+Cb) has   784 elements
> Group 7 (MainChain+H) has   785 elements
> Group 8 (  SideChain) has   803 elements
> Group 9 (SideChain-H) has   612 elements
> Group10 (Prot-Masses) has  1588 elements
> Group11 (non-Protein) has 27049675 elements
> Group12 (  Other) has59 elements
> Group13 (ACO) has59 elements
> Group14 ( NA) has 16615 elements
> Group15 ( CL) has 16615 elements
> Group16 (  Water) has 27016386 elements
> Group17 (SOL) has 27016386 elements
> Group18 (  non-Water) has 34877 elements
> Group19 (Ion) has 33230 elements
> Group20 (ACO) has59 elements
> Group21 ( NA) has 16615 elements
> Group22 ( CL) has 16615 elements
> Group23 ( Water_and_ions) has 27049616 elements
> Group24 (
>
> Now how can I be able to get both Protein+ACO as a pdb file ?
> If I could get Protein+ACO, then I could strip the box size for further
> umbrella sampling procedure.
>
> However, is it possible to go with the following way:
> editconf_mpi -f confout1.gro -o conf_1.gro -c -d 1.0 -bt cubic
>
> Please suggest me a way.
>
> Thank you.
>
> On Mon, Apr 24, 2017 at 1:38 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Take a configuration of interest, strip the solvent, put it in a box you
> > think is good, and re-equilibrate just like you did before you started.
> >
> > Mark
> >
> > On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > > Yes, I did when I started the simulation. The box size I used to start
> > the
> > > simulation was very big(I was dealing with an unknown sample). After
> > > successfully generating the configurations I realized that further work
> > > could move faster if I could trim the box size little bit now.
> > > So is there any way now to reduce the box size and proceed with
> relevant
> > > configurations towards PMF generation ?
> > > Please suggest me a way here.
> > >
> > > Thank you.
> > >
> > > On Apr 24, 2017 12:22 AM, "Mark Abraham" 
> > wrote:
> > >
> > > > Hi,
> > > >
> > > > You get to choose the box size eg with editconf when you set up your
> > > > simulation. It's not pre-defined ;-)
> > > >
> > > > Mark
> > > >
> > > > On Sun, 23 Apr 2017 20:28 abhisek Mondal 
> > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Another thing I wanted to ask.
> > > > > After generating configurations I found out that the predefined box
> > > size
> > > > > (used to reach so far) is excessively high.
> > > > > Is it possible to trim the box size to perform further mdrun during
> > > > > umbrella sampling?
> > > > >
> > > > > Please suggest me a way, it is taking very long time with current
> box
> > > > size.
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
> > > > >
> > > > > On Apr 23, 2017 10:02 PM, "Mark Abraham"  >
> > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > You can only load a trajectory with fewer frames. Either don't
> > write
> > > so
> > > > > > many, or filter it with trjconv first.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, 23 Apr 2017 17:20 abhisek Mondal  >
> > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > > I'm having a problem loading trajectory file after umbrella
> > > sampling.
> > > > > The
> > > > > > > file is so huge in size that the VMD finally runs out of
> memory.
> > > I'm
> > > > > > > operating with 125gb of physical memory here though.
> > > > > > >
> > > > > > > Is there any way out of it ?
> > > > > > >
> > > > > > >
> > > > > > > Thank you
> > > > > > > --
> > > > > > > Abhisek Mondal
> > > > > > >
> > > > > > > *Senior Research Fellow*
> > > > > > >
> > > > > > > *Structural Biology and Bioinformatics Division*
> > > > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > > > >
> > > > 

Re: [gmx-users] powercut command

[Tasneem Kausar]

For md.xtc output -x flag is there. -o flag gives the md.trr as output.
This is what Gromacs is complaining.


File name 'md_1_0.xtc' cannot be used for this option.
Only the following extensions are possible:

On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <anshullahariy...@gmail.com
> wrote:

> powercut take place and md stops, so i want to continue my md
>
>
>
>
> [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> Karkoulis
> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
>Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
>   Teemu Virolainen  Christian WennbergMaarten Wolf
>and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS:  gmx mdrun, version 2016.2
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /home/anshu/Pharma/AhpE_MSH
> Command line:
>   gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc -cpi
> md_1_0.cpt -cpo md_1_0.cpt -append
>
>
> ---
> Program: gmx mdrun, version 2016.2
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -o
> File name 'md_1_0.xtc' cannot be used for this option.
> Only the following extensions are possible:
>   .trr, .cpt, .tng
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> [root@dhcppc58 AhpE_MSH]# ^C
> [root@dhcppc58 AhpE_MSH]#
>
>
>
>
> plzzz help me and suggest me the command for continuation of my md run
>
> On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <tasneemkausa...@gmail.com
> >
> wrote:
>
> > please give the exact command and error message.
> >
> > On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
> > anshullahariy...@gmail.com
> > > wrote:
> >
> > > dear das sir,
> > >
> > > -cpi was already added to the command but my problem is not solved
> > >
> > > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
> > > anshullahariy...@gmail.com
> > > > wrote:
> > >
> > > > error says, xtc file is not used for this option . plzz use trr, cpt,
> > tng
> > > >
> > > >
> > > > help me out
> > > >
> > > > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com>
> > wrote:
> > > >
> > > >> please put this command line
> > > >> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi
> xxx.cpt
> > -o
> > > >> md_1_0.xtc
> > > >>
> > > >> good luck
> > > >>
> > > >> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
> > > >> anshullahariy...@gmail.com> wrote:
> > > >>
> > > >> > My md was running. Suddenly power supply was cuts due to some
> reason
> > > >> and my
> > > >> > my MD stops..
> > > >> > To continue my MD, I use command:-
> > > >> >
> > > >> >
> > > >> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
> > > 10ns.cpt
> > > >> > -cpo 10ns.cpt 

Re: [gmx-users] powercut command

[Tasneem Kausar]

gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
-cpo 10ns.cpt -append
There is problem in the command that you have given in your first mail.

gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -x 10ns.xtc -cpi 10ns.cpt
-append

You did not provided the -x flag. This was the reason for error

On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> please give the exact command and error message.
>
> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
> anshullahariy...@gmail.com> wrote:
>
>> dear das sir,
>>
>> -cpi was already added to the command but my problem is not solved
>>
>> On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
>> anshullahariy...@gmail.com
>> > wrote:
>>
>> > error says, xtc file is not used for this option . plzz use trr, cpt,
>> tng
>> >
>> >
>> > help me out
>> >
>> > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com> wrote:
>> >
>> >> please put this command line
>> >> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt
>> -o
>> >> md_1_0.xtc
>> >>
>> >> good luck
>> >>
>> >> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
>> >> anshullahariy...@gmail.com> wrote:
>> >>
>> >> > My md was running. Suddenly power supply was cuts due to some reason
>> >> and my
>> >> > my MD stops..
>> >> > To continue my MD, I use command:-
>> >> >
>> >> >
>> >> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
>> 10ns.cpt
>> >> > -cpo 10ns.cpt -append
>> >> >
>> >> >
>> >> >
>> >> > but shows error.
>> >> >
>> >> >
>> >> > Error in user input:
>> >> > Invalid command-line options
>> >> > Unknown command-line option -md_1_0.xtc
>> >> >
>> >> > For more information and tips for troubleshooting, please check the
>> >> GROMACS
>> >> > website at http://www.gromacs.org/Documentation/Errors
>> >> > ---
>> >> > [root@dhcppc58 AhpE_MSH]#
>> >> >
>> >> >
>> >> >
>> >> > Plzz.. help me out
>> >> > --
>> >> > Gromacs Users mailing list
>> >> >
>> >> > * Please search the archive at http://www.gromacs.org/
>> >> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >> >
>> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> >
>> >> > * For (un)subscribe requests visit
>> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> >> > send a mail to gmx-users-requ...@gromacs.org.
>> >> >
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at http://www.gromacs.org/Support
>> >> /Mailing_Lists/GMX-Users_List before posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>> >
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] powercut command

[Tasneem Kausar]

please give the exact command and error message.

On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya  wrote:

> dear das sir,
>
> -cpi was already added to the command but my problem is not solved
>
> On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
> anshullahariy...@gmail.com
> > wrote:
>
> > error says, xtc file is not used for this option . plzz use trr, cpt, tng
> >
> >
> > help me out
> >
> > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb  wrote:
> >
> >> please put this command line
> >> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o
> >> md_1_0.xtc
> >>
> >> good luck
> >>
> >> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
> >> anshullahariy...@gmail.com> wrote:
> >>
> >> > My md was running. Suddenly power supply was cuts due to some reason
> >> and my
> >> > my MD stops..
> >> > To continue my MD, I use command:-
> >> >
> >> >
> >> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
> 10ns.cpt
> >> > -cpo 10ns.cpt -append
> >> >
> >> >
> >> >
> >> > but shows error.
> >> >
> >> >
> >> > Error in user input:
> >> > Invalid command-line options
> >> > Unknown command-line option -md_1_0.xtc
> >> >
> >> > For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> > website at http://www.gromacs.org/Documentation/Errors
> >> > ---
> >> > [root@dhcppc58 AhpE_MSH]#
> >> >
> >> >
> >> >
> >> > Plzz.. help me out
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
> >> > Support/Mailing_Lists/GMX-Users_List before posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
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> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> --
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Re: [gmx-users] COMMAND IN HBOND

[Tasneem Kausar]

If you want to calculate hydrogen bond invloving residue there are two steps
>From gmx hbond you can obtain an xpm file where hydrogen bond existance mad
is plotted.  Then calculate the percentage of hydrogen bond involving
residues from script given by justin.
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Re: [gmx-users] Pull code grompp error

[Tasneem Kausar]

Define you pull group in index file  as the error message says.

On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary 
wrote:

> Hi,
>
> Below is my .mdp code for pulling as found in the tutorial by Justin
> Lemkul. I made the required changes to match my version syntax.
>
> pull= umbrella
> pull_ngroups= 2
> pull_group0= Protein_chain_A
> pull_group1= DNA_chain_B
> pull_group2= DNA_chain_C
> pull_geometry= distance  ; simple distance increase
> pull_dim = Y N N
> pull_rate1= 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_rate2= 0.01
> pull_k1   = 1000  ; kJ mol^-1 nm^-2
> pull_k2   = 1000
> pull_start   = yes   ; define initial COM distance > 0
>
> When I tried to grompp using this code, it generates an error:
>
> Fatal error:
> Group topol_Protein_chain_A referenced in the .mdp file was not found in
> the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> I searched for the solutions in the Gromacs forum and found it might be due
> to name mismatch. But, in my case, the names are exactly same as referenced
> in the *.mdp file. Below is the molecule names from the topol.top file.
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DNA_chain_B 1
> DNA_chain_C 1
> SOL 33542
> NA   125
> CL   98
>
> Can you please help to solve the problem? I tried with changing the names
> to Protein and DNA (the residue types) and changing the ngroups to 3.
> Nothing worked.
>
> Regards,
>
> Souparno Adhikary
> University of Calcutta,
> India.
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Re: [gmx-users] Error in free energy calculation

[Tasneem Kausar]

Thank you everyone for your reply.

I have resolved the problem for reply of Justin from previous mail at gmx
list.

Thank you Justin again

On Thu, Mar 16, 2017 at 5:57 PM, Amir Zeb <zebami...@gmail.com> wrote:

> You probably follow umbrella sampling for free energy calculation.
> If it is so, you may change the position of your drug.itp file in topology
> file, means that before the protein topology.
> I hope this might solve your problem.
>
> Good luck!
>
> Amir
>
> On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar <tasneemkausa...@gmail.com
> >
> wrote:
>
> > Dear All
> >
> > I am trying to perform free energy calculations of a protein drug system.
> > I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e.
> drug
> > molecule is defined in separate drug.itp file. From the discussions of
> > mailing list I have found that this is not a problem. To obtain the
> > equilibrium values for protein-ligand restraint 15 ns simulation was
> > performed. Here is the last section of topology file.
> >  ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> > #include "drug.itp"
> > [ intermolecular_interactions ]
> > [ bonds ]
> > ;i j  type r0A r1A r2AfcAr0B r1B r2B
> > fcB
> >   1444  311810 0.591   0.591   10.0   0.00.591   0.591   10.0
> > 4184.000
> >
> > [ angle_restraints ]
> > ;   aiajakal  typethA  fcAmultA  thB  fcB
> > multB
> >   1431  1444  3118  1444 152.350.0152.3541.840
>   1
> >   1444  3118  3120  3118 1   118.140.01   118.1441.840
>   1
> >
> > [ dihedral_restraints ]
> > ;   aiajakal  typephiA dphiA  fcAphiB  dphiB
> > fcB
> >   1444  1431  1444  3118 1-99.41   0.00.0-99.410.0
> > 41.840
> >   1431  1444  3118  3120 1 17.490.00.017.490.0
> > 41.840
> >   1444  3118  3120  3119 1 -6.49   0.00.0 -6.490.0
> > 41.840
> > ; Include water topology
> > #include "gromos54a7.ff/spc.itp"
> >
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ;  i funct   fcxfcyfcz
> >11   1000   1000   1000
> > #endif
> >
> > ; Include topology for ions
> > #include "gromos54a7.ff/ions.itp"
> >
> > [ system ]
> > ; Name
> > DUMM in water t= 1.0
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DRG 1
> > SOL 17685
> >
> > Is there any default position for [ intermolecular_interaction ] in
> > topology file.
> > Since I am using a drug.itp file for drug molecule. Numbering in itp file
> > starts from 1. Is atom number in itp file needed to be modified?
> >
> >
> > grompp gives many warning  and 1 error
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
> >
> > WARNING 1 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_geometry' in parameter file
> >
> >
> >
> > WARNING 2 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_dim' in parameter file
> >
> >
> >
> > WARNING 3 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_start' in parameter file
> >
> >
> >
> > WARNING 4 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_init1' in parameter file
> >
> >
> >
> > WARNING 5 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_ngroups' in parameter file
> >
> >
> >
> > WARNING 6 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_group0' in parameter file
> >
> >
> >
> > WARNING 7 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_group1' in parameter file
> >
> >
> >
> > WARNING 8 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_k1' in parameter file
> >
> >
> >
> > WARNING 9 [file em_steep_0.mdp, line 78]:
> >   Unknown left-hand 'pull_kB1' in parameter file
> >
> >
> >
> > NOTE 1 [file em_steep_0.mdp]:
> >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> >   that with the Verlet scheme, nstlist has no effect on the accuracy of
> >   your simulation.
> >
> > Setting the LD random seed to 1259182625
> &g

[gmx-users] Error in free energy calculation

[Tasneem Kausar]

Dear All

I am trying to perform free energy calculations of a protein drug system.
I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug
molecule is defined in separate drug.itp file. From the discussions of
mailing list I have found that this is not a problem. To obtain the
equilibrium values for protein-ligand restraint 15 ns simulation was
performed. Here is the last section of topology file.
 ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#include "drug.itp"
[ intermolecular_interactions ]
[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
fcB
  1444  311810 0.591   0.591   10.0   0.00.591   0.591   10.0
4184.000

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
multB
  1431  1444  3118  1444 152.350.0152.3541.8401
  1444  3118  3120  3118 1   118.140.01   118.1441.8401

[ dihedral_restraints ]
;   aiajakal  typephiA dphiA  fcAphiB  dphiB
fcB
  1444  1431  1444  3118 1-99.41   0.00.0-99.410.0
41.840
  1431  1444  3118  3120 1 17.490.00.017.490.0
41.840
  1444  3118  3120  3119 1 -6.49   0.00.0 -6.490.0
41.840
; Include water topology
#include "gromos54a7.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos54a7.ff/ions.itp"

[ system ]
; Name
DUMM in water t= 1.0
[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG 1
SOL 17685

Is there any default position for [ intermolecular_interaction ] in
topology file.
Since I am using a drug.itp file for drug molecule. Numbering in itp file
starts from 1. Is atom number in itp file needed to be modified?


grompp gives many warning  and 1 error
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#

WARNING 1 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_geometry' in parameter file



WARNING 2 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_dim' in parameter file



WARNING 3 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_start' in parameter file



WARNING 4 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_init1' in parameter file



WARNING 5 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_ngroups' in parameter file



WARNING 6 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_group0' in parameter file



WARNING 7 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_group1' in parameter file



WARNING 8 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_k1' in parameter file



WARNING 9 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_kB1' in parameter file



NOTE 1 [file em_steep_0.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1259182625
Generated 226 of the 1711 non-bonded parameter combinations

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/shahid/Software/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
line: 755

Fatal error:
Syntax error - File complex.top, line 19956
Last line read:
'[ intermolecular_interactions ]'
Invalid order for directive intermolecular_interactions
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here are mdp parameters

; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no
sc-power = 1
sc-sigma = 0.3
couple-moltype   = DRG
couple-lambda0   = none
couple-lambda1   = vdw-q
couple-intramol  = no
nstdhdl  = 10
; No velocities during EM
gen_vel  = no
; options for bonds
constraints  = all_bonds
constraint-algorithm = lincs
continuation = no
lincs-order  = 12
pull   = no
pull_geometry  = distance
pull_dim   = N N Y
pull_start = yes
pull_init1 = 0.654
pull_ngroups   = 1
pull_group0= a_1444
pull_group1= a_3118
pull_k1= 0.0   ; kJ*mol^(-1)*nm^(-2)
pull_kB1   = 4184  ; kJ*mol^(-1)*nm^(-2)

since I have defined restraint parameters for protein and drug. then what
is need of pulling code and why?

Kindly resolve the issue.
Thanks in Advance.
Regards
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Re: [gmx-users] Adding a number of drugs around a polymer

[Tasneem Kausar]

Check gmx insert

On 25 Feb 2017 18:12, "faride badalkhani"  wrote:

> Dear GROMACS users,
>
> I need to locate a number of drug molecules around one equilibrated polymer
> molecule and drugs should be randomly located within a spherical shell from
> the polymer surface.
> Will be greatly appreciated if help me on that.
>
> Regards,
> Farideh
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Re: [gmx-users] Extending a program

[Tasneem Kausar]

No its not needed.
gmx convert-tpr will serve the perpose. In -extend option you can specify
the extension (50ns/100ns).

On Thu, Feb 23, 2017 at 4:33 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Okay
>
> In case I need to extend another 50ns should change mdp?
>
>
>
> On Thu, 23 Feb 2017 at 3:21 PM, Tasneem Kausar <tasneemkausa...@gmail.com>
> wrote:
>
> > If you have state.cpt file from the previous simulation, on extending the
> > simulation -cpi state.cpt will serve to read the last coordinate of your
> > previous simulation.
> >  Use this command
> > gmx mdrun -v -deffnm extend.tpr -cpi state.cpt
> >
> > On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > dear Amir
> > > it is mandatory to change the mdp file?
> > >
> > > And what change should i do in that?
> > >
> > > On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb <zebami...@gmail.com>
> wrote:
> > >
> > > > Hello Rahul,
> > > >
> > > > Just extend the simulation time in mdp file and repeat the same
> > commands
> > > as
> > > > you done for early 100 ns.
> > > >
> > > > Best!
> > > >
> > > > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com>
> > > > wrote:
> > > >
> > > > > I have a 100ns simulated file.(md.xtc) I need to extend to another
> > 100
> > > > ns.
> > > > >
> > > > > do i need to make any change to mdp file.?
> > > > >
> > > > > I used the command
> > > > >
> > > > >
> > > > >
> > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr*
> > > > >
> > > > > *gmx mdrun -v -deffnm extend.tpr*
> > > > >
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
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> > > >
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] Extending a program

[Tasneem Kausar]

If you have state.cpt file from the previous simulation, on extending the
simulation -cpi state.cpt will serve to read the last coordinate of your
previous simulation.
 Use this command
gmx mdrun -v -deffnm extend.tpr -cpi state.cpt

On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH 
wrote:

> dear Amir
> it is mandatory to change the mdp file?
>
> And what change should i do in that?
>
> On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb  wrote:
>
> > Hello Rahul,
> >
> > Just extend the simulation time in mdp file and repeat the same commands
> as
> > you done for early 100 ns.
> >
> > Best!
> >
> > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH 
> > wrote:
> >
> > > I have a 100ns simulated file.(md.xtc) I need to extend to another 100
> > ns.
> > >
> > > do i need to make any change to mdp file.?
> > >
> > > I used the command
> > >
> > >
> > >
> > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr*
> > >
> > > *gmx mdrun -v -deffnm extend.tpr*
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] deformation in simulation

[Tasneem Kausar]

here is whole command
gmx trjconv -f production.xtc -s protein.tpr -o production_pbc.xtc -pbc
whole

On Thu, Feb 23, 2017 at 3:13 PM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> You should apply periodic boundary condition on your protein.
> check gmx trjconv -h and selcet (-pbc whole)
>
> First load protein.gro file in vmd. In vmd main window molecule
> information is given. Write click on that and then click load data into
> molecule option. Select protein.xtc file. It will load the trajectory of
> protein snapshots.
>
> On Thu, Feb 23, 2017 at 2:42 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> wrote:
>
>> Dear Amir
>>
>> Only pdb files are being displayed in vmd
>> Xtc files are there. They run but there s no display
>>
>> I have simulated
>>
>>
>>
>>
>>
>>
>> On Thu, 23 Feb 2017 at 1:43 PM, Amir Zeb <zebami...@gmail.com> wrote:
>>
>> > first you let me know, you have produced your md run or not?
>> > xtc file is the output of md production, if you didn't actually simulate
>> > yet, how can you get xtc file?
>> >
>> > On Thu, Feb 23, 2017 at 12:07 AM, RAHUL SURESH <drrahulsur...@gmail.com
>> >
>> > wrote:
>> >
>> > > again why XTC files are not being displayed in vmd
>> > > ?
>> > >
>> > >
>> > > On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb <zebami...@gmail.com>
>> wrote:
>> > >
>> > > > so what did you find?
>> > > > Did you fix the problem?
>> > > >
>> > > > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K <
>> subashi...@hotmail.com
>> > >
>> > > > wrote:
>> > > >
>> > > > > Many tutorials suggest to run two equilibrations and then
>> production
>> > > > file.
>> > > > >
>> > > > >
>> > > > > At first, run a restrained equilibrium.
>> > > > >
>> > > > >
>> > > > > Then non-restrained equilibrium followed by production file.
>> > > > >
>> > > > >
>> > > > > Do not know the aim of your simulations.
>> > > > >
>> > > > >
>> > > > > Hope this answer helps.
>> > > > >
>> > > > >
>> > > > > Thanks,
>> > > > >
>> > > > > Subashini.K
>> > > > >
>> > > > > 
>> > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
>> > RAHUL
>> > > > > SURESH <drrahulsur...@gmail.com>
>> > > > > Sent: Thursday, February 23, 2017 12:23 PM
>> > > > > To: gmx-us...@gromacs.org
>> > > > > Subject: [gmx-users] deformation in simulation
>> > > > >
>> > > > > Simulating a protein with 100residues for 200ns doesn't show any
>> > > > stability.
>> > > > > There are some deformation(long-bonds) in the structure throughout
>> > the
>> > > > > process. Why is that so? Can I choose any stable structure in
>> between
>> > > > these
>> > > > > 200ns, for example say 176ns. Or is there any other way to make
>> them
>> > > work
>> > > > > good.I need your valuable suggestions
>> > > > >
>> > > > > --
>> > > > > *Regards,*
>> > > > > *Rahul Suresh*
>> > > > > *Research Scholar*
>> > > > > *Bharathiar University*
>> > > > > *Coimbatore*
>> > > > > --
>> > > > > Gromacs Users mailing list
>> > > > >
>> > > > > * Please search the archive at http://www.gromacs.org/
>> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
>> > > > >
>> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > > >
>> > > > > * For (un)subscribe requests visit
>> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>> -users
>> > or
>> > > > > send a mail to gmx-users-requ...@gromacs.org.
>> > > > > gromacs.org_gmx-users Info Page - Royal Institute of ...<
>> > &g

Re: [gmx-users] deformation in simulation

[Tasneem Kausar]

You should apply periodic boundary condition on your protein.
check gmx trjconv -h and selcet (-pbc whole)

First load protein.gro file in vmd. In vmd main window molecule information
is given. Write click on that and then click load data into molecule
option. Select protein.xtc file. It will load the trajectory of protein
snapshots.

On Thu, Feb 23, 2017 at 2:42 PM, RAHUL SURESH 
wrote:

> Dear Amir
>
> Only pdb files are being displayed in vmd
> Xtc files are there. They run but there s no display
>
> I have simulated
>
>
>
>
>
>
> On Thu, 23 Feb 2017 at 1:43 PM, Amir Zeb  wrote:
>
> > first you let me know, you have produced your md run or not?
> > xtc file is the output of md production, if you didn't actually simulate
> > yet, how can you get xtc file?
> >
> > On Thu, Feb 23, 2017 at 12:07 AM, RAHUL SURESH 
> > wrote:
> >
> > > again why XTC files are not being displayed in vmd
> > > ?
> > >
> > >
> > > On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb  wrote:
> > >
> > > > so what did you find?
> > > > Did you fix the problem?
> > > >
> > > > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K <
> subashi...@hotmail.com
> > >
> > > > wrote:
> > > >
> > > > > Many tutorials suggest to run two equilibrations and then
> production
> > > > file.
> > > > >
> > > > >
> > > > > At first, run a restrained equilibrium.
> > > > >
> > > > >
> > > > > Then non-restrained equilibrium followed by production file.
> > > > >
> > > > >
> > > > > Do not know the aim of your simulations.
> > > > >
> > > > >
> > > > > Hope this answer helps.
> > > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Subashini.K
> > > > >
> > > > > 
> > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> > RAHUL
> > > > > SURESH 
> > > > > Sent: Thursday, February 23, 2017 12:23 PM
> > > > > To: gmx-us...@gromacs.org
> > > > > Subject: [gmx-users] deformation in simulation
> > > > >
> > > > > Simulating a protein with 100residues for 200ns doesn't show any
> > > > stability.
> > > > > There are some deformation(long-bonds) in the structure throughout
> > the
> > > > > process. Why is that so? Can I choose any stable structure in
> between
> > > > these
> > > > > 200ns, for example say 176ns. Or is there any other way to make
> them
> > > work
> > > > > good.I need your valuable suggestions
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > gromacs.org_gmx-users Info Page - Royal Institute of ...<
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >
> > > > > maillist.sys.kth.se
> > > > > gromacs.org_gmx-users -- Discussion list for GROMACS users About
> > > > > gromacs.org_gmx-users
> > > > >
> > > > >
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> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > >
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
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> > * Please 

Re: [gmx-users] gmx trjcat

[Tasneem Kausar]

See options with gmx trjcat -h

On Thu, Feb 23, 2017 at 8:49 AM, YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
>  I have a long trajectory , which is broken into 2 part because of
> disk space : traj 1  is 0ns-213ns, the other traj 2  is 200ns-300ns. How to
> concatenate this two trajectory into one single file trj 3(0ns-300ns) with
> trjcat since they have overlapping times(200ns-214ns)? how can I keep one
> of the overlapping time appropriately?
>
> Best regards,
> Ouyang.
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Re: [gmx-users] Hydrogen bond problem

[Tasneem Kausar]

Thank you for reply
I am using Justin's perl script for calculating hydrogen bond existence. I
am following the same procedure like deleting all the above lines before
[hbond_protein_drug] and using pdb file with no chain ID etc. I have read
the out file of hbm and hbn  also. Then what could be the problem.

On Wed, Feb 8, 2017 at 3:20 PM, Erik Marklund <erik.markl...@kemi.uu.se>
wrote:

> Dera Tasneem,
>
> First thing to check is if you have read the -hbn or -hbm output upside
> down. This is a common mistake. Seriously.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD
> Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC
> Uppsala Universtity
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>
> On 8 Feb 2017, at 06:06, Tasneem Kausar <tasneemkausa...@gmail.com tasneemkausa...@gmail.com>> wrote:
>
> Dear all
>
> I am calculating hydrogen bond between protein and drug molecule using gmx
> hbond tool. I am using default value for hydrogen bond radius.
> Here is the command:
> gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm
> hbond.ndx
> I am selecting group 1 and 13.
> It shows many hydrogen bonds. Then I have calculated the percentage of
> hydrogen bond using perl script. There are there hydrogen bonds that show a
> significant existence. I wrote the snapshots of trajectories having all
> three hydrogen bonds. In every snapshot, when visulaized with a
> visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin
> does not exist though it shows hydrophobic interaction with drug molecule.
> LIGPLUS gives a provision to show the missing hydrogen bond. When I have
> plotted by taking consideration serin hydrogen bond, it shows a bond length
> of 4.26 angstrom and like that in almost every extracted snapshot. In
> existence map serin is showing 92% abundance of hydrogen bond. This problem
> is occurring with serin only.
>
> Why is this happening? Is there a cut off problem with the visualization
> tools or something else?
>
> Is there an method to write the hydrogen bond and there distance
> simultaneously.
>
> Thanks in Advance
> Tasneem
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[gmx-users] Hydrogen bond problem

[Tasneem Kausar]

Dear all

I am calculating hydrogen bond between protein and drug molecule using gmx
hbond tool. I am using default value for hydrogen bond radius.
Here is the command:
gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm
hbond.ndx
I am selecting group 1 and 13.
It shows many hydrogen bonds. Then I have calculated the percentage of
hydrogen bond using perl script. There are there hydrogen bonds that show a
significant existence. I wrote the snapshots of trajectories having all
three hydrogen bonds. In every snapshot, when visulaized with a
visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin
does not exist though it shows hydrophobic interaction with drug molecule.
LIGPLUS gives a provision to show the missing hydrogen bond. When I have
plotted by taking consideration serin hydrogen bond, it shows a bond length
of 4.26 angstrom and like that in almost every extracted snapshot. In
existence map serin is showing 92% abundance of hydrogen bond. This problem
is occurring with serin only.

Why is this happening? Is there a cut off problem with the visualization
tools or something else?

Is there an method to write the hydrogen bond and there distance
simultaneously.

Thanks in Advance
 Tasneem
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Re: [gmx-users] Gro file does not match topology file... continue

[Tasneem Kausar]

You both are right. Previously I was editing the topology file after
solvating the protein.
So the mismatch error was there.


Sorry for the inconvenience...



On Sat, Jan 28, 2017 at 7:14 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 1/27/17 8:39 PM, Tasneem Kausar wrote:
>
>> Yes , you are right. I was also surprised that when atoms in gro and
>> topology match then how this error can be.
>> In my case I was simulating a small peptide segment in water. Everything
>> goes smoothly in it. Then I have generated a system with 8 peptides using
>> genconf command.
>> I have generated a box with editconf with -d 1.1 in a cubical box. In last
>> line of topology file protein_chain_A was changed from 1 to 8. The genbox
>> was used to solvate the system. Then grompp gives  the mismatch error.
>> Then with a box size of 2.1grompp was executed without any error.
>> Same mdp file was used in both the case.
>>
>> This is the whole procedure, I have followed.
>>
>> This is why I was saying to increase the box size.
>>
>>
> Without exact commands and error messages, there's no way to know what
> happened except that whatever mistake you made the first time, you didn't
> make the second.  "Increase the box size" is not a solution for a mismatch
> between coordinates and topology.  Correct bookkeeping is.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Gro file does not match topology file... continue

[Tasneem Kausar]

Yes , you are right. I was also surprised that when atoms in gro and
topology match then how this error can be.
In my case I was simulating a small peptide segment in water. Everything
goes smoothly in it. Then I have generated a system with 8 peptides using
genconf command.
I have generated a box with editconf with -d 1.1 in a cubical box. In last
line of topology file protein_chain_A was changed from 1 to 8. The genbox
was used to solvate the system. Then grompp gives  the mismatch error.
Then with a box size of 2.1grompp was executed without any error.
Same mdp file was used in both the case.

This is the whole procedure, I have followed.

This is why I was saying to increase the box size.

Thanks
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Re: [gmx-users] Gro file does not match topology file... continue

[Tasneem Kausar]

I was having the same problem. The atoms in topology and gro were same and
this error was there. By increasing box size the problem was resolved.
What would be tge reason for that.?

On 27 Jan 2017 22:30, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 1/27/17 11:48 AM, Tasneem Kausar wrote:
>
>> Increase your box size.
>>
>>
> Changing the box will not solve this issue.  If you make a mismatched
> system bigger, it's still mismatched.
>
> -Justin
>
> On 27 Jan 2017 22:15, "Poncho Arvayo Zatarain" <poncho_8...@hotmail.com>
>> wrote:
>>
>>
>>>
>>> Hello: according to the queshere abouttion and the answer send me here
>>> about gro (58674) file does not mtch with the topology (58666), i checked
>>> my gro file at the top corner on the left and said 58674, and at the end
>>> of
>>> the file the number of molecules is the same, 58674. i used TIP3 model
>>> and
>>> 2 phospholipids: 26 dppe and 230 dppe also 8960 of TIP3.
>>> My top file is
>>> : Include forcefield parameters
>>> #include "toppar/charmm36.itp"
>>> #include "toppar/compound.itp"
>>> #include "toppar/DPPC.itp"
>>> #include "toppar/DPPE.itp"
>>> #include "toppar/TIP3.itp"
>>>
>>> [System]
>>> : Name
>>> Title
>>>
>>> [Molecules]
>>> : Compound #mols
>>> COMPOUND72
>>> DPPE230
>>> DPPC26
>>> TIP3  8960
>>> --
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>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
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> http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] Gro file does not match topology file... continue

[Tasneem Kausar]

Increase your box size.

On 27 Jan 2017 22:15, "Poncho Arvayo Zatarain" 
wrote:

>
>
> Hello: according to the queshere abouttion and the answer send me here
> about gro (58674) file does not mtch with the topology (58666), i checked
> my gro file at the top corner on the left and said 58674, and at the end of
> the file the number of molecules is the same, 58674. i used TIP3 model and
> 2 phospholipids: 26 dppe and 230 dppe also 8960 of TIP3.
> My top file is
> : Include forcefield parameters
> #include "toppar/charmm36.itp"
> #include "toppar/compound.itp"
> #include "toppar/DPPC.itp"
> #include "toppar/DPPE.itp"
> #include "toppar/TIP3.itp"
>
> [System]
> : Name
> Title
>
> [Molecules]
> : Compound #mols
> COMPOUND72
> DPPE230
> DPPC26
> TIP3  8960
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Re: [gmx-users] VMD

[Tasneem Kausar]

May be atom number of your xtc and gro file are not same. Write a new gro
file with the same output you are taking for
xtc after skiping the frames.

On 25 Jan 2017 17:38, "Mark Abraham"  wrote:

> Hi,
>
> Indeed. But unless someone knows what you did with trjconv, and how you
> used VMD differently, it will probably stay a mystery.
>
> Mark
>
> On Wed, 25 Jan 2017 11:49 RAHUL SURESH  wrote:
>
> > Thank you mark.
> >
> > I think this problem prevails for many users. I came across a user forum
> > and found same issues.
> >
> > Anyway Thank you.
> >
> > On Wed, Jan 25, 2017 at 3:32 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > We can't guess.
> > >
> > > Mark
> > >
> > > On Wed, 25 Jan 2017 09:01 RAHUL SURESH 
> wrote:
> > >
> > > > I tried that too but there is no visual
> > > >
> > > > Why is t.?
> > > > On Wed, 25 Jan 2017 at 1:07 PM,  wrote:
> > > >
> > > > > Hi Rahul,
> > > > >
> > > > >
> > > > >
> > > > > VMD ran out of memory. Try using trjconv to create a new xtc with a
> > > > subset
> > > > >
> > > > > of atoms or a subset of frames.
> > > > >
> > > > >
> > > > >
> > > > > Best wishes
> > > > >
> > > > > James
> > > > >
> > > > >
> > > > >
> > > > > > I tried to visualize my xtc on VMD and the job get killed at 7000
> > > > frames
> > > > >
> > > > > >
> > > > >
> > > > > > why is that so?
> > > > >
> > > > > >
> > > > >
> > > > > > --
> > > > >
> > > > > > *Regards,*
> > > > >
> > > > > > *Rahul Suresh*
> > > > >
> > > > > > *Research Scholar*
> > > > >
> > > > > > *Bharathiar University*
> > > > >
> > > > > > *Coimbatore*
> > > > >
> > > > > > --
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[tasneem kausar]

My be ACPYP added missing hydrogen. It is better to use top and gro file of
from the same source.
Try editconf from the ACPYP gro file. The topology file may need some
modifications accordingly.

On Thu, Jan 19, 2017 at 12:30 PM, Subashini .K <subashi...@hotmail.com>
wrote:

> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
>
> The ligand contains only 29 atoms.
>
>
> But, in the top and gro generated by acpype it shows 31 atoms.
>
>
> There lies the problem.
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Amir Zeb <
> zebami...@gmail.com>
> Sent: Thursday, January 19, 2017 12:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> Hello
> review the number of atoms in gro file and top file
> also check that the 2nd line in gro file showing the total number of atoms
> should be in parallel with all the atoms existed in the gro file
> this way you may solve the problem
> good luck
>
> On Jan 19, 2017 3:20 PM, "Subashini .K" <subashi...@hotmail.com> wrote:
>
> > Hi,
> >
> >
> >
> > Thank you for the reply. As I said earlier, there is one ligand molecule
> > surrounded by many water molecules (680)
> >
> >
> > Here, it is like this
> >
> >
> > [ molecules ]
> > ; Compoundnmols
> >  ligand   1
> >  WAT  680
> >
> >
> > 680 seems to be a correct number. Because, it was computed as follows,
> > using tleap of AMBER TOOLS 15:
> >
> >
> > solvateBox LIG TIP4PBOX 10.0
> >  Solute vdw bounding box:  9.963 8.173 7.953
> >   Total bounding box for atom centers:  29.963 28.173 27.953
> >   Solvent unit box: 18.860 18.867 18.860
> >   Total vdw box size:   33.150 30.999 31.097 angstroms.
> >   Volume: 31955.384 A^3
> >   Total mass 12429.154 amu,  Density 0.646 g/cc
> >   Added 680 residues.
> >
> > Still, there is an error.
> >
> >
> > --------
> > 
> > 
> > -
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> > kausar <tasneemkausa...@gmail.com>
> > Sent: Thursday, January 19, 2017 11:04 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
> >
> > The error show that the number of atoms in topology file and gro file
> does
> > not match
> > In last line of topology file define the ligand molecule.
> > here is the exapmle
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DRG 1
> >
> >
> >
> >
> > On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > >
> > > Had taken one organic molecule (ligand) and many water molecules using
> > > tleap of Amber tools 15.
> > >
> > >
> > > Then generated .top and .gro file using acpype by the command,
> > >
> > > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> > >
> > >
> > > However, while using the same for gromacs, obtained the following error
> > >
> > >
> > > number of coordinates in coordinate file (conf.gro, 2751)
> > >  does not match topology (topol.top, 2071)
> > >
> > > How to fix this error?
> > >
> > > Thanks,
> > > Subashini.K
> >
> > --
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[tasneem kausar]

In topology file the name of ligand defined in  [ moleculetype ] section
and at the end of file as [ molecules ]
 should be same.
Hope this will help you.

On Thu, Jan 19, 2017 at 11:50 AM, Subashini .K <subashi...@hotmail.com>
wrote:

> Hi,
>
>
>
> Thank you for the reply. As I said earlier, there is one ligand molecule
> surrounded by many water molecules (680)
>
>
> Here, it is like this
>
>
> [ molecules ]
> ; Compoundnmols
>  ligand   1
>  WAT  680
>
>
> 680 seems to be a correct number. Because, it was computed as follows,
> using tleap of AMBER TOOLS 15:
>
>
> solvateBox LIG TIP4PBOX 10.0
>  Solute vdw bounding box:  9.963 8.173 7.953
>   Total bounding box for atom centers:  29.963 28.173 27.953
>   Solvent unit box: 18.860 18.867 18.860
>   Total vdw box size:   33.150 30.999 31.097 angstroms.
>   Volume: 31955.384 A^3
>   Total mass 12429.154 amu,  Density 0.646 g/cc
>   Added 680 residues.
>
> Still, there is an error.
>
>
> 
> 
> 
> -
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> kausar <tasneemkausa...@gmail.com>
> Sent: Thursday, January 19, 2017 11:04 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> The error show that the number of atoms in topology file and gro file does
> not match
> In last line of topology file define the ligand molecule.
> here is the exapmle
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DRG 1
>
>
>
>
> On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> wrote:
>
> > Hi gromacs users,
> >
> >
> > Had taken one organic molecule (ligand) and many water molecules using
> > tleap of Amber tools 15.
> >
> >
> > Then generated .top and .gro file using acpype by the command,
> >
> > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> >
> >
> > However, while using the same for gromacs, obtained the following error
> >
> >
> > number of coordinates in coordinate file (conf.gro, 2751)
> >  does not match topology (topol.top, 2071)
> >
> > How to fix this error?
> >
> > Thanks,
> > Subashini.K
>
> --
> Gromacs Users mailing list
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> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] REGARDING TOPOLOGY FILE

[tasneem kausar]

The error show that the number of atoms in topology file and gro file does
not match
In last line of topology file define the ligand molecule.
here is the exapmle

[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG 1




On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K 
wrote:

> Hi gromacs users,
>
>
> Had taken one organic molecule (ligand) and many water molecules using
> tleap of Amber tools 15.
>
>
> Then generated .top and .gro file using acpype by the command,
>
> acpype -p com_solvated.top -x com_solvated.crd -b ligand
>
>
> However, while using the same for gromacs, obtained the following error
>
>
> number of coordinates in coordinate file (conf.gro, 2751)
>  does not match topology (topol.top, 2071)
>
> How to fix this error?
>
> Thanks,
> Subashini.K
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Topology parameters for ligand

[tasneem kausar]

Thank You for your reply

The system under my study has positive charge. There are 3 positive charges
on the protein and one on drug molecule. How these charges will be handled.


On Mon, Jan 9, 2017 at 6:37 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 1/9/17 2:31 AM, tasneem kausar wrote:
>
>> I got it.
>>
>> I have looked at the input files for the T4-lysozyme tutorial available at
>> alchemistry.org. They have defined state A and state B. I am using
>> GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
>> decoupling parameters are taken from the mdp options, like by defining
>> [lambda-moltype] in mdp file. As I know from the tutorials and manual the
>> solvation free energy of the ligand can calculated.
>>
>> From the alchemistry.org input files, the topology parameters of ligand
>> are
>> inserted in protein topology named as complex.top.
>>
>> If I follow the same protocol without defining the state B of the ligand
>> in
>> topology, how the ligand molecule will be decoulped in complex.
>>
>>
> An explicit B-state is necessary for a relative free energy calculation,
> in which one molecule is transformed into another.
>
> For any absolute free energy calculation (solvation, binding, etc) then
> you do not need to define a B-state, and just couple the physical
> parameters to lambda to turn them on/off.
>
> -Justin
>
>
>
>>
>> On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 1/7/17 10:29 PM, tasneem kausar wrote:
>>>
>>> Thank you for your reply
>>>>
>>>> In last section of your tutorial you have suggested some changes to made
>>>> in
>>>> mdp file. That can be used for solvation free energies.
>>>> For free energy calculation of protein drug complex, is it only lambda
>>>> restraint to be defined?
>>>>
>>>>
>>>> Along with a complex system of [intermolecular_interactions] that
>>> preserve
>>> the relative orientation of the ligand.  This is a very complex
>>> calculation
>>> in practice.  See examples on alchemistry.org and in the literature in
>>> works by Roux, Im, Karplus, etc.  My tutorial is not very useful for such
>>> calculations; it is extremely basic relative to what is needed to carry
>>> out
>>> a binding free energy calculation.  I only mentioned it there because so
>>> many people asked about it and I wanted to clear up any confusion.
>>>
>>> -Justin
>>>
>>>
>>> On 8 Jan 2017 01:45, "Justin Lemkul" <jalem...@vt.edu> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 1/7/17 6:05 AM, tasneem kausar wrote:
>>>>>
>>>>> Dear all
>>>>>
>>>>>>
>>>>>> I am following Justin's tutorial methane in water for free energy
>>>>>> calculation. I am using Gromacs-5.1.4. The charges of methane in
>>>>>> topology
>>>>>> are set to zero. So following the same protocol, is it relevant to set
>>>>>> the
>>>>>> charges at zero in topology of the drug. I am confused because in
>>>>>> tutorial
>>>>>> of Sander (ethanol in water) charges are present in the topology file.
>>>>>>
>>>>>> Please tell me the difference in both the tutorials and how can I
>>>>>> apply
>>>>>> it
>>>>>> to drug that I want to study.
>>>>>>
>>>>>>
>>>>>> The charges in my tutorial are set to zero because the stated goal of
>>>>>>
>>>>> that
>>>>> tutorial is to reproduce *only the LJ portion of the hydration free
>>>>> energy*
>>>>> to match a published paper.  This creates a very simple, robust system.
>>>>> If
>>>>> you want to calculate a real, meaningful hydration or binding free
>>>>> energy,
>>>>> charge transformation is required.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>>

Re: [gmx-users] Topology parameters for ligand

[tasneem kausar]

I got it.

I have looked at the input files for the T4-lysozyme tutorial available at
alchemistry.org. They have defined state A and state B. I am using
GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
decoupling parameters are taken from the mdp options, like by defining
[lambda-moltype] in mdp file. As I know from the tutorials and manual the
solvation free energy of the ligand can calculated.

>From the alchemistry.org input files, the topology parameters of ligand are
inserted in protein topology named as complex.top.

If I follow the same protocol without defining the state B of the ligand in
topology, how the ligand molecule will be decoulped in complex.



On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 1/7/17 10:29 PM, tasneem kausar wrote:
>
>> Thank you for your reply
>>
>> In last section of your tutorial you have suggested some changes to made
>> in
>> mdp file. That can be used for solvation free energies.
>> For free energy calculation of protein drug complex, is it only lambda
>> restraint to be defined?
>>
>>
> Along with a complex system of [intermolecular_interactions] that preserve
> the relative orientation of the ligand.  This is a very complex calculation
> in practice.  See examples on alchemistry.org and in the literature in
> works by Roux, Im, Karplus, etc.  My tutorial is not very useful for such
> calculations; it is extremely basic relative to what is needed to carry out
> a binding free energy calculation.  I only mentioned it there because so
> many people asked about it and I wanted to clear up any confusion.
>
> -Justin
>
>
> On 8 Jan 2017 01:45, "Justin Lemkul" <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 1/7/17 6:05 AM, tasneem kausar wrote:
>>>
>>> Dear all
>>>>
>>>> I am following Justin's tutorial methane in water for free energy
>>>> calculation. I am using Gromacs-5.1.4. The charges of methane in
>>>> topology
>>>> are set to zero. So following the same protocol, is it relevant to set
>>>> the
>>>> charges at zero in topology of the drug. I am confused because in
>>>> tutorial
>>>> of Sander (ethanol in water) charges are present in the topology file.
>>>>
>>>> Please tell me the difference in both the tutorials and how can I apply
>>>> it
>>>> to drug that I want to study.
>>>>
>>>>
>>>> The charges in my tutorial are set to zero because the stated goal of
>>> that
>>> tutorial is to reproduce *only the LJ portion of the hydration free
>>> energy*
>>> to match a published paper.  This creates a very simple, robust system.
>>> If
>>> you want to calculate a real, meaningful hydration or binding free
>>> energy,
>>> charge transformation is required.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] Topology parameters for ligand

[tasneem kausar]

Thank you for your reply

In last section of your tutorial you have suggested some changes to made in
mdp file. That can be used for solvation free energies.
For free energy calculation of protein drug complex, is it only lambda
restraint to be defined?

On 8 Jan 2017 01:45, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 1/7/17 6:05 AM, tasneem kausar wrote:
>
>> Dear all
>>
>> I am following Justin's tutorial methane in water for free energy
>> calculation. I am using Gromacs-5.1.4. The charges of methane in topology
>> are set to zero. So following the same protocol, is it relevant to set the
>> charges at zero in topology of the drug. I am confused because in tutorial
>> of Sander (ethanol in water) charges are present in the topology file.
>>
>> Please tell me the difference in both the tutorials and how can I apply it
>> to drug that I want to study.
>>
>>
> The charges in my tutorial are set to zero because the stated goal of that
> tutorial is to reproduce *only the LJ portion of the hydration free energy*
> to match a published paper.  This creates a very simple, robust system.  If
> you want to calculate a real, meaningful hydration or binding free energy,
> charge transformation is required.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Topology parameters for ligand

[tasneem kausar]

Dear all

I am following Justin's tutorial methane in water for free energy
calculation. I am using Gromacs-5.1.4. The charges of methane in topology
are set to zero. So following the same protocol, is it relevant to set the
charges at zero in topology of the drug. I am confused because in tutorial
of Sander (ethanol in water) charges are present in the topology file.

Please tell me the difference in both the tutorials and how can I apply it
to drug that I want to study.


Thanks in Advance
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks again

That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.

Waiting for your suggestion

On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb <zebami...@gmail.com> wrote:

> well
> if you are confident of your simulation you may definitly go ahead with
> this ff
> otherwise you will have to change the ff for simulation too
> i think this is not rational to simulate the system with one ff and then
> change the ff for free energy calculations
>
> good luck
>
> On Jan 7, 2017 2:01 PM, "tasneem kausar" <tasneemkausa...@gmail.com>
> wrote:
>
> > Thanks Amir Zeb for your reply
> > I have read in literature about the FEPsetup to parametrize the complex
> > file (protein+drug) for simulation. This setup builds files based on
> amber.
> > Since I have previously used 54a7ff to simulate the protein and drug and
> > topology files were generated from ATB in gromos54a7 format. Since I
> didn't
> > find free energy calculation of protein and ligand with this force field.
> > Thats why I was confused to proceed further using the same.
> >
> > On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <
> tasneemkausa...@gmail.com
> > >
> > wrote:
> >
> > > mm/pbsa calculates binding energy. I have used that.
> > >
> > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote:
> > >
> > >> hello
> > >> you may use mm/pbsa compiled with gromacs to calculate free energy
> > >> all the best
> > >>
> > >> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausa...@gmail.com>
> > >> wrote:
> > >>
> > >> > Dear gromacs users
> > >> >
> > >> > It is first time I am trying to perform free energy calculation of
> > >> protein
> > >> > and drug complex. I am following Justin' s tutorial of mehtane in
> > water.
> > >> > That calculation are performed on a neutral system. If the ligand
> > >> molecule
> > >> > has charge what are the provisions that could be taken into account.
> > >> > I have performed my MD simulation using force field gromos54a7. And
> > Now
> > >> I
> > >> > am trying to go onward using free energy calculations. Since the
> free
> > >> > energy calculations are performed on ambed99ldn, opls and charmm
> force
> > >> > fields (as I know from the articles). Is it okay to use gromos54a7
> ff
> > >> for
> > >> > free energy calculations.
> > >> >
> > >> > Kindly tell me
> > >> >
> > >> > Thanks in Advance
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at http://www.gromacs.org/
> > >> > Support/Mailing_Lists/GMX-Users_List before posting!
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> or
> > >> > send a mail to gmx-users-requ...@gromacs.org.
> > >> >
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromos54a7 format. Since I didn't
find free energy calculation of protein and ligand with this force field.
Thats why I was confused to proceed further using the same.

On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <tasneemkausa...@gmail.com>
wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote:
>
>> hello
>> you may use mm/pbsa compiled with gromacs to calculate free energy
>> all the best
>>
>> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausa...@gmail.com>
>> wrote:
>>
>> > Dear gromacs users
>> >
>> > It is first time I am trying to perform free energy calculation of
>> protein
>> > and drug complex. I am following Justin' s tutorial of mehtane in water.
>> > That calculation are performed on a neutral system. If the ligand
>> molecule
>> > has charge what are the provisions that could be taken into account.
>> > I have performed my MD simulation using force field gromos54a7. And Now
>> I
>> > am trying to go onward using free energy calculations. Since the free
>> > energy calculations are performed on ambed99ldn, opls and charmm force
>> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
>> for
>> > free energy calculations.
>> >
>> > Kindly tell me
>> >
>> > Thanks in Advance
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
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>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
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>
>
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

mm/pbsa calculates binding energy. I have used that.

On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote:

> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar" <tasneemkausa...@gmail.com>
> wrote:
>
> > Dear gromacs users
> >
> > It is first time I am trying to perform free energy calculation of
> protein
> > and drug complex. I am following Justin' s tutorial of mehtane in water.
> > That calculation are performed on a neutral system. If the ligand
> molecule
> > has charge what are the provisions that could be taken into account.
> > I have performed my MD simulation using force field gromos54a7. And Now I
> > am trying to go onward using free energy calculations. Since the free
> > energy calculations are performed on ambed99ldn, opls and charmm force
> > fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> > free energy calculations.
> >
> > Kindly tell me
> >
> > Thanks in Advance
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Dear gromacs users

It is first time I am trying to perform free energy calculation of protein
and drug complex. I am following Justin' s tutorial of mehtane in water.
That calculation are performed on a neutral system. If the ligand molecule
has charge what are the provisions that could be taken into account.
I have performed my MD simulation using force field gromos54a7. And Now I
am trying to go onward using free energy calculations. Since the free
energy calculations are performed on ambed99ldn, opls and charmm force
fields (as I know from the articles). Is it okay to use gromos54a7 ff for
free energy calculations.

Kindly tell me

Thanks in Advance
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[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Dear all

It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein under my study have positive charges (one positive charge on ligand
and tree positive charges on protein). So I have to add a CL ions in
topology file to make a neutral sytem.
Is it okay to use the system with ion for free energy calculation?
If yes, What are change that can be made in mdp entry.

Waiting for suggestions
Thanks in Advance
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[gmx-users] Free energy calculation of protein and ligand

[tasneem kausar]

Dear all

It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein under my study have positive charges (one positive charge on ligand
and tree positive charges on protein). So I have to add a CL ions in
topology file to make a neutral sytem.
Is it okay to use the system with ion for free energy calculation?
If yes, What are change that can be made in mdp entry.

Waiting for suggestions
Thanks in Advance
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[gmx-users] Free energy calculation of protein and ligand

[tasneem kausar]

Dear all

It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein under my study have positive charges (one positive charge on ligand
and tree positive charges on protein). So I have to add a CL ions in
topology file to make a neutral sytem.
Is it okay to use the system with ion for free energy calculation?
If yes, What are change that can be made in mdp entry.

Waiting for suggestions
Thanks in Advance
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[gmx-users] Free energy calculation of protein and ligand

[tasneem kausar]

Dear all

It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein under my study have positive charges (one positive charge on ligand
and tree positive charges on protein). So I have to add a CL ions in
topology file to make a neutral sytem.
Is it okay to use the system with ion for free energy calculation?
If yes, What are change that can be made in mdp entry.

Waiting for suggestions
Thanks in Advance
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Re: [gmx-users] DMSO

[tasneem kausar]

Check the total number of atoms in DMSO molecule.
after grompp you got an error of non-matching atom in gro and top file.
Subtract the number of molecule of top  file from molecule of gro file.
Divide the subtracted number with coordinates of DMSO. This gives the
number of DMSO molecule. Add this number to the top file.

Hope this will help

On Tue, Dec 20, 2016 at 9:38 PM, Hoda Alibiglou 
wrote:

> Hello
>
> I am simulating a protein in mixture of water and DMSO, I madE the box
> including water and DMSO and my protein, now I should add ions by this
> command,
>
>
> gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr
>
> but, each time I get an error because the number of atoms in my
> topology file and
>
> dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
> DMSO molecules number manually, now my error is that DMSO is unknown,
> also I used some references and according them I choosed gromos96
> forcefield for DMSO-WATER MIXTURE.
>
> may I ask you please to help me ?
>
> Best regards,
>
> Hoda
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Re: [gmx-users] Charge on drug

[tasneem kausar]

Thank you
I have generated the itp file from ATB. It works fine.


On Wed, Dec 21, 2016 at 7:48 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/19/16 1:23 PM, tasneem kausar wrote:
>
>> Thank you for reply
>> What type of refinements are needed in topolgy file.
>> I have created the topology file from pdb file. Mol2 was converted into
>> pdb
>> and sdf of pubchem was converted into mol2.
>> So sdf to mol2 to pdb.
>> And please suggest me the right choice of server for itp file generation.
>>
>>
> Check the bond length parameters and make sure your coordinate file
> matches the order of the atoms in the topology.  Don't ignore warnings from
> grompp.
>
> -Justin
>
>
> Thanks in advance
>>
>> On 19 Dec 2016 18:31, "Justin Lemkul" <jalem...@vt.edu> wrote:
>>
>>>
>>>
>>>
>>> On 12/19/16 5:31 AM, tasneem kausar wrote:
>>>
>>>>
>>>> Thanks for reply
>>>>
>>>> I have visualized solvate.gro and em.gro. Some bonds that are not
>>>> present
>>>> in box.gro is seen in em.gro.
>>>> I am giving you the link of the file to visualize.
>>>> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
>>>> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
>>>>
>>>
>>>
>>> You have an amide group that distorts, bringing the carbonyl C closer to
>>>
>> the amide proton, which VMD then fictitiously assigns as a C-H bond.  The
>> C-N bond is much too short.  This suggests your topology is of
>> insufficient
>> quality for doing simulations and requires refinement.  There is, of
>> course, no actual bond there, as Mark has pointed out.  Visualization
>> software tries to guess where bonds should be based on interatomic
>> distances.  The topology is definitive. What you see on your screen is
>> not.
>>
>>>
>>>
>>> I addition to that I have done energy minimization multiple times with
>>>> steepest decent and conjugate gradient method. Potential energy value is
>>>> negative in every minimization. When I am trying position restrain core
>>>> dump with multiple lincs warning occurs.
>>>>
>>>
>>>
>>> Your topology needs work.  It will not be stable for any simulation.
>>>
>>> -Justin
>>>
>>>
>>> Please tell me how this problem would be resolved
>>>>
>>>> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abra...@gmail.com
>>>> >
>>>> wrote:
>>>>
>>>> Hi,
>>>>>
>>>>> Your energy minimization literally cannot create bonds because those
>>>>> are
>>>>> already defined by your topology. See
>>>>>
>>>>> http://www.gromacs.org/Downloads/Related_Software/Visualizat
>> ion_Software#
>>
>>> Topology_bonds_vs_Rendered_bonds
>>>>> for what's probably going on.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com>
>>>>> wrote:
>>>>>
>>>>> Dear All
>>>>>>
>>>>>>
>>>>>> I am using Acpype server to generate topology file of drug molecule to
>>>>>> perform protein drug MD simulation. Acpype have generated the itp file
>>>>>>
>>>>>
>>>>> and
>>>>>
>>>>>>
>>>>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>>>>>>
>>>>>
>>>>> software
>>>>>
>>>>>>
>>>>>> using amber99sb force field. When I have done energy minimization some
>>>>>> unwanted bonds are formed in drug molecule. So the position restraint
>>>>>>
>>>>> is
>>
>>> not able to execute. The problem is due to the unusual bond in drug
>>>>>>
>>>>> atom.
>>
>>> When I used the itp file of PRODRG server position restraint goes
>>>>>> successfully. I have used the gromos54a7 ff. But there is problem with
>>>>>>
>>>>>
>>>>> the
>>>>>
>>>>>>
>>>>>> charge present on the atom that comes from PRODRG.
>>>>>>
>>>>>> Please tell me how charge on the at

Re: [gmx-users] Charge on drug

[tasneem kausar]

Thank you for reply
What type of refinements are needed in topolgy file.
I have created the topology file from pdb file. Mol2 was converted into pdb
and sdf of pubchem was converted into mol2.
So sdf to mol2 to pdb.
And please suggest me the right choice of server for itp file generation.

Thanks in advance

On 19 Dec 2016 18:31, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>
> On 12/19/16 5:31 AM, tasneem kausar wrote:
>>
>> Thanks for reply
>>
>> I have visualized solvate.gro and em.gro. Some bonds that are not present
>> in box.gro is seen in em.gro.
>> I am giving you the link of the file to visualize.
>> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
>> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
>
>
> You have an amide group that distorts, bringing the carbonyl C closer to
the amide proton, which VMD then fictitiously assigns as a C-H bond.  The
C-N bond is much too short.  This suggests your topology is of insufficient
quality for doing simulations and requires refinement.  There is, of
course, no actual bond there, as Mark has pointed out.  Visualization
software tries to guess where bonds should be based on interatomic
distances.  The topology is definitive. What you see on your screen is not.
>
>
>> I addition to that I have done energy minimization multiple times with
>> steepest decent and conjugate gradient method. Potential energy value is
>> negative in every minimization. When I am trying position restrain core
>> dump with multiple lincs warning occurs.
>
>
> Your topology needs work.  It will not be stable for any simulation.
>
> -Justin
>
>
>> Please tell me how this problem would be resolved
>>
>> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Your energy minimization literally cannot create bonds because those are
>>> already defined by your topology. See
>>>
http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
>>> Topology_bonds_vs_Rendered_bonds
>>> for what's probably going on.
>>>
>>> Mark
>>>
>>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com>
>>> wrote:
>>>
>>>> Dear All
>>>>
>>>>
>>>> I am using Acpype server to generate topology file of drug molecule to
>>>> perform protein drug MD simulation. Acpype have generated the itp file
>>>
>>> and
>>>>
>>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>>>
>>> software
>>>>
>>>> using amber99sb force field. When I have done energy minimization some
>>>> unwanted bonds are formed in drug molecule. So the position restraint
is
>>>> not able to execute. The problem is due to the unusual bond in drug
atom.
>>>> When I used the itp file of PRODRG server position restraint goes
>>>> successfully. I have used the gromos54a7 ff. But there is problem with
>>>
>>> the
>>>>
>>>> charge present on the atom that comes from PRODRG.
>>>>
>>>> Please tell me how charge on the atom can be corrected in itp file of
>>>> PRODRG.  How the problem in energy minimization with the Acpype itp
will
>>>
>>> be
>>>>
>>>> resolved.
>>>>
>>>> Thanks in Advance
>>>> With Regards
>>>> Tasneem
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
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>>>>
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>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirs

Re: [gmx-users] Charge on drug

[tasneem kausar]

solvate.gro is box.gro file. It was typing mistake.

On Mon, Dec 19, 2016 at 4:01 PM, tasneem kausar <tasneemkausa...@gmail.com>
wrote:

> Thanks for reply
>
> I have visualized solvate.gro and em.gro. Some bonds that are not present
> in box.gro is seen in em.gro.
> I am giving you the link of the file to visualize.
> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
> I addition to that I have done energy minimization multiple times with
> steepest decent and conjugate gradient method. Potential energy value is
> negative in every minimization. When I am trying position restrain core
> dump with multiple lincs warning occurs.
> Please tell me how this problem would be resolved
>
> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
>> Hi,
>>
>> Your energy minimization literally cannot create bonds because those are
>> already defined by your topology. See
>> http://www.gromacs.org/Downloads/Related_Software/Visualizat
>> ion_Software#Topology_bonds_vs_Rendered_bonds
>> for what's probably going on.
>>
>> Mark
>>
>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com>
>> wrote:
>>
>> > Dear All
>> >
>> >
>> > I am using Acpype server to generate topology file of drug molecule to
>> > perform protein drug MD simulation. Acpype have generated the itp file
>> and
>> > other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>> software
>> > using amber99sb force field. When I have done energy minimization some
>> > unwanted bonds are formed in drug molecule. So the position restraint is
>> > not able to execute. The problem is due to the unusual bond in drug
>> atom.
>> > When I used the itp file of PRODRG server position restraint goes
>> > successfully. I have used the gromos54a7 ff. But there is problem with
>> the
>> > charge present on the atom that comes from PRODRG.
>> >
>> > Please tell me how charge on the atom can be corrected in itp file of
>> > PRODRG.  How the problem in energy minimization with the Acpype itp
>> will be
>> > resolved.
>> >
>> > Thanks in Advance
>> > With Regards
>> > Tasneem
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
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>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
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>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
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>
>
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Re: [gmx-users] Charge on drug

[tasneem kausar]

Thanks for reply

I have visualized solvate.gro and em.gro. Some bonds that are not present
in box.gro is seen in em.gro.
I am giving you the link of the file to visualize.
https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
I addition to that I have done energy minimization multiple times with
steepest decent and conjugate gradient method. Potential energy value is
negative in every minimization. When I am trying position restrain core
dump with multiple lincs warning occurs.
Please tell me how this problem would be resolved

On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Your energy minimization literally cannot create bonds because those are
> already defined by your topology. See
> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
> Topology_bonds_vs_Rendered_bonds
> for what's probably going on.
>
> Mark
>
> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com>
> wrote:
>
> > Dear All
> >
> >
> > I am using Acpype server to generate topology file of drug molecule to
> > perform protein drug MD simulation. Acpype have generated the itp file
> and
> > other necessary for MD simulations. I am doing MD on gromacs 5.1.4
> software
> > using amber99sb force field. When I have done energy minimization some
> > unwanted bonds are formed in drug molecule. So the position restraint is
> > not able to execute. The problem is due to the unusual bond in drug atom.
> > When I used the itp file of PRODRG server position restraint goes
> > successfully. I have used the gromos54a7 ff. But there is problem with
> the
> > charge present on the atom that comes from PRODRG.
> >
> > Please tell me how charge on the atom can be corrected in itp file of
> > PRODRG.  How the problem in energy minimization with the Acpype itp will
> be
> > resolved.
> >
> > Thanks in Advance
> > With Regards
> > Tasneem
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] Charge on drug

[tasneem kausar]

Dear All


I am using Acpype server to generate topology file of drug molecule to
perform protein drug MD simulation. Acpype have generated the itp file and
other necessary for MD simulations. I am doing MD on gromacs 5.1.4 software
using amber99sb force field. When I have done energy minimization some
unwanted bonds are formed in drug molecule. So the position restraint is
not able to execute. The problem is due to the unusual bond in drug atom.
When I used the itp file of PRODRG server position restraint goes
successfully. I have used the gromos54a7 ff. But there is problem with the
charge present on the atom that comes from PRODRG.

Please tell me how charge on the atom can be corrected in itp file of
PRODRG.  How the problem in energy minimization with the Acpype itp will be
resolved.

Thanks in Advance
With Regards
Tasneem
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[gmx-users] Charge Correction using HF method

[tasneem kausar]

Dear
Justin Sir

I am doing protein and drug MD simulation. I have generated the itp file of
drug from PRODRG. I have calculated the charge on the atom using HF/6- 31G*
basis set from orca3.0. Is this a right protocol to use it in GROMACS for
the charge correction.

With Regards
Tasneem
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[gmx-users] Problem in mdrun

[tasneem kausar]

Dear All

I am performing MD simulation of protein and drug in Gromacs_4.5.4 using
amber99SB force field with tip3p water model. I have successfully generated
the tpr file for full MD simulation with two drugs. I have some other drugs
to simulate with the same protein. Everything goes smoothly till the energy
minimization giving a negative potential energy value. When I am try to run
position restrain, mdrun is not generating any output. There is no error or
warning massage. I have enough disk space of around 125 GB. I have tried
mdrun at another PC and also at Gromacs_4.6.3.

Here is my mdp file for position restrain.
;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
constraintalgorithm =  LINCS
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5; total 100 ps.
nstcomm =  1
nstxout =  500
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9
coulombtype =  PME
rcoulomb=  0.9
rvdw=  1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps=  ProteinNon-protein
tau_t   =  0.10.1
ref_t   =  300300
; Energy monitoring
energygrps=  ProteinNon-protein
; Pressure coupling is not on
Pcoupl  =  no
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

Kindly tell me where I am missing.

Thanks in advance.

With Regards
Tasneem Kausar
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Re: [gmx-users] (no subject)

[tasneem kausar]

Dear Kingsley

You are directly calculating the rms after combining the xtc file. It is
clear from the warning that you did not apply perodic boundary condition on
you trajectory.

Try trjconv -f combined.xtc -s refrence.tpr -o combined_pbc.xtc -pbc whole
-center command after trjcat. After trjconv calculate RMS.


On Sat, Nov 19, 2016 at 11:06 AM, Kingsley Theras Primus Dass . <
105726...@gms.tcu.edu.tw> wrote:

> Dear Users!!
>
>
>  I have a question about RMSD.  I ran MＤ simulaton for 500ns and connected
> all my .xtc files using trjcat command.
> And , then I used g_rms command with the connected .xtc file to calculate
> RMSD for backbone atoms. But , when I run g_rms command , I get a warning
> as follows:
>
>
>
> WARNING: If there are molecules in the input trajectory file
>  that are broken across periodic boundaries, they
>  cannot be made whole (or treated as whole) without
>  you providing a run input file.
>
> Can someone say , why this warning msg is coming, and how should i need to
> avoid this. what measure should i need to take ?
>
>
>
>
> Thank you.
> --
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Re: [gmx-users] MD simulations of two chains protein

[tasneem kausar]

I have suggested you in previous mail to plot chain A and chain B
separately. I have looked at the link. It is because of the same residue
number in chain A and chain B. In xvg file chain identifier (A/B) will not
be shown. Just open .xvg file in any text editor. Copy the residue number
and their corresponding rmsd values of chain A. Paste it in orgin software
or excel and plot. Do the same for chain B residues.
  Make_ndx option of gromacs can also help you. Make index file for chain A
and chain B. Calculate RMSF of chain A and then RMSF of chain B.
Hope this will help you.


On Thu, Nov 17, 2016 at 1:07 PM, Khadija Amine  wrote:

> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Wed, Nov 16, 2016 at 9:15 AM, Khadija Amine 
> wrote:
>
> > Hi Mark,
> >
> > Below, the link to the rmsf plot I had for my protein throughout 20 ns
> > simulation.
> >
> > https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0
> >
> > The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq
> > rmsf.pdb -res
> >
> > Thank you
> >
> > *Khadija AMINE*
> >
> >
> > *Computational Biology*
> > *Postdoctoral Research Associate*
> > *Carnegie Mellon University*
> >
> > On Tue, Nov 15, 2016 at 10:50 AM, Khadija Amine 
> > wrote:
> >
> >> Ok I will try that.
> >>
> >> There is a way to specify the regions to plot in RMSF using rms tool?
> >>
> >> Thank you
> >>
> >> *Khadija AMINE*
> >>
> >>
> >> *Computational Biology*
> >> *Postdoctoral Research Associate*
> >> *Carnegie Mellon University*
> >>
> >> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine 
> >> wrote:
> >>
> >>> Hello,
> >>>
> >>> Can someone show me how can I proceed?
> >>>
> >>> Thank you
> >>>
> >>> *Khadija AMINE*
> >>>
> >>>
> >>> *Computational Biology*
> >>> *Postdoctoral Research Associate*
> >>> *Carnegie Mellon University*
> >>>
> >>> On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine 
> >>> wrote:
> >>>
>  Dear Gromacs users,
> 
>  I need your help regarding MD simulation of two chains protein.
>  The chain A is 2-78 aa, and the chain B is 1-168 aa.
> 
>  I started with the pdb file where there is specified names of the two
>  chains as A and B.
> 
>  I did solvation of my system in a cubic box, I tried to open the
>  pdb file issued from this step I didn't find the column specifying the
>  chain names.
> 
>  I run 20 ns of MD for this protein. The RMSF plot of the protein seems
>  to be overlapping from 1 to 78 and the rest of the residues flctuation
>  is good.
> 
>  As it is the first time am facing such issues with protein with two
>  chains, how can I avoid such overlap in RMSF plot?
> 
>  Is this linked to the chains numbering issued after writing the
>  topology.
> 
>  Thank you
> 
>  *Khadija AMINE*
> 
> 
>  *Computational Biology*
>  *Postdoctoral Research Associate*
>  *Carnegie Mellon University*
> 
> >>>
> >>>
> >>
> >
> --
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Re: [gmx-users] MD simulations of two chains protein

[tasneem kausar]

Plot chain A and chain B separately. Residue no. in both the chain are
started from 1. It will overlap in same plot.

On Mon, Nov 14, 2016 at 5:03 PM, Khadija Amine  wrote:

> Dear Gromacs users,
>
> I need your help regarding MD simulation of two chains protein.
> The chain A is 2-78 aa, and the chain B is 1-168 aa.
>
> I started with the pdb file where there is specified names of the two
> chains as A and B.
>
> I did solvation of my system in a cubic box, I tried to open the pdb file
> issued from this step I didn't find the column specifying the chain names.
>
> I run 20 ns of MD for this protein. The RMSF plot of the protein seems to
> be overlapping from 1 to 78 and the rest of the residues flctuation is
> good.
>
> As it is the first time am facing such issues with protein with two chains,
> how can I avoid such overlap in RMSF plot?
>
> Is this linked to the chains numbering issued after writing the topology.
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
> --
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Re: [gmx-users] trr file

[tasneem kausar]

Hi
I think you can try analysis in more than one step by using -b and -e
option of trjconv.

On Fri, Oct 14, 2016 at 5:59 PM, Mark Abraham 
wrote:

> Hi,
>
> Prevention is the best medicine - ask google about reducing GROMACS
> trajectory storage volume :-)
>
> Mark
>
> On Fri, Oct 14, 2016 at 1:20 PM Nuno Azoia  wrote:
>
> > Have you tried the option -split?
> > I never tried, and I don't know if it will solve your problem, but give
> it
> > a try.
> >
> >
> > On Fri, Oct 14, 2016 at 11:34 AM, Rita Paiva Melo <
> > ritam...@ctn.tecnico.ulisboa.pt> wrote:
> >
> > > Hello,
> > >
> > > Thank you for your suggestions. I have already tried run trjconv but,
> as
> > > trajectory is heavy and server is full, out of memory error appears and
> > > analysis tool crash.
> > >
> > > Best,
> > > Rita.
> > >
> > > -Original Message-
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Nuno
> > Azoia
> > > Sent: 14 de outubro de 2016 11:19
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] trr file
> > >
> > > Hello Rita,
> > >
> > > I think the answer is trjconv. Try to convert it to xtc, reduce the
> > number
> > > of frames (with dt or skip), or reduce the components on the
> trajectory.
> > If
> > > you don't need solvent for the calculations you can create a trajectory
> > > without it. Removing the solvent and convert it to xtc should have a
> > great
> > > impact in file size.
> > >
> > > Nuno Azoia
> > >
> > > On Fri, Oct 14, 2016 at 11:04 AM, Rita Paiva Melo <
> > > ritam...@ctn.tecnico.ulisboa.pt> wrote:
> > >
> > > > Dear all,
> > > >
> > > > Probably a rookie question but anyone knows how to reduce trajectory
> > > > volume file to be analyzed (I have already tried trjconv)? I have a
> > > > trr file with  167 GB and analysis tools crash.
> > > >
> > > > Thanks,
> > > > Rita.
> > > >
> > > > --
> > > > Gromacs Users mailing list
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> > > >
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Re: [gmx-users] Protein Drug simulation Parameters

[tasneem kausar]

I have modified the trajectory running the trjconv command in three steps.
First trjconv is with -pbc whole, second is -pbc nojump with respect to
first frame and third is centering the the protein and drug. the output of
first step is provided as input in the second step and so on. When I am
calculating the RMSD of C-alpha atom for protein and C-alpha atom of
protein+drug their RMSD plot overlaps. However mmpbsa energy calculated
from this trajectory shows positive binding energy.
As RMSD plot of protein and protein+drug overlap suggests stable binding of
drug with protein then why the mmpbsa energy is positive and vice versa and
what is the reason behind it. I did not do -pbc cluster and -ur compact
with the trajectory as I am getting nice trajectory with these three option
on visualization.  Moreover I wish someone should give me some reading
materials on use of pbc options and its influence on binding energy.



On Tue, Sep 27, 2016 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/27/16 7:32 AM, tasneem kausar wrote:
>
>> Thank you Justin for your reply.
>> There is another question regarding MMPBSA energy calculations. I have
>> calculated the MMPBSA energy of 8 potential protein+drug complex.
>> Simulation time was 50 ns. One of the protein drug complex gives the
>> positive binding energy. Does the periodic boundary conditions like whole
>> and nojump effect the binding energy.
>>
>>
> Of course.  You need to provide sensible configurations to analyze.  If
> the trajectory is not imaged properly, the results will be nonsense.  But
> of course, it is simple to tell if the input trajectory is OK - watch it.
>
> -Justin
>
>
> On Mon, Sep 26, 2016 at 5:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 9/26/16 4:43 AM, tasneem kausar wrote:
>>>
>>> Dear All
>>>>
>>>> I have performed MD simulation of protein and drug crystal structure. I
>>>> have generated drug  itp file from PRODRG server and corrected the
>>>> charges
>>>> of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
>>>> 2221–2235.
>>>> I have done 50 ns MD simulation of protein and drug using g43a1 force
>>>> field
>>>> and spc water model. After 15 ns drug molecule comes out of the pocket.
>>>> Is this expected during MD simulation. If this occurs what is the reason
>>>> behind it.
>>>> Should we change any specific parameter for protein drug simulation.
>>>>
>>>>
>>>> First, make sure it is not a simple periodicity issue by re-imaging the
>>> trajectory with trjconv.  Several iterations will likely be necessary;
>>> see
>>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions#Suggested_trjconv_workflow
>>>
>>> If there is some legitimate problem that leads to ligand dissociation,
>>> either your run settings are inappropriate, the initial geometry has
>>> large
>>> clashes that lead to large forces that expel the ligand, or the ligand
>>> topology is incorrect and overly attracted to the bulk aqueous
>>> environment.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
&g

Re: [gmx-users] Protein Drug simulation Parameters

[tasneem kausar]

Thank you Justin for your reply.
There is another question regarding MMPBSA energy calculations. I have
calculated the MMPBSA energy of 8 potential protein+drug complex.
Simulation time was 50 ns. One of the protein drug complex gives the
positive binding energy. Does the periodic boundary conditions like whole
and nojump effect the binding energy.

On Mon, Sep 26, 2016 at 5:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/26/16 4:43 AM, tasneem kausar wrote:
>
>> Dear All
>>
>> I have performed MD simulation of protein and drug crystal structure. I
>> have generated drug  itp file from PRODRG server and corrected the charges
>> of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
>> 2221–2235.
>> I have done 50 ns MD simulation of protein and drug using g43a1 force
>> field
>> and spc water model. After 15 ns drug molecule comes out of the pocket.
>> Is this expected during MD simulation. If this occurs what is the reason
>> behind it.
>> Should we change any specific parameter for protein drug simulation.
>>
>>
> First, make sure it is not a simple periodicity issue by re-imaging the
> trajectory with trjconv.  Several iterations will likely be necessary; see
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions#Suggested_trjconv_workflow
>
> If there is some legitimate problem that leads to ligand dissociation,
> either your run settings are inappropriate, the initial geometry has large
> clashes that lead to large forces that expel the ligand, or the ligand
> topology is incorrect and overly attracted to the bulk aqueous environment.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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[gmx-users] Protein Drug simulation Parameters

[tasneem kausar]

Dear All

I have performed MD simulation of protein and drug crystal structure. I
have generated drug  itp file from PRODRG server and corrected the charges
of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
2221–2235.
I have done 50 ns MD simulation of protein and drug using g43a1 force field
and spc water model. After 15 ns drug molecule comes out of the pocket.
Is this expected during MD simulation. If this occurs what is the reason
behind it.
Should we change any specific parameter for protein drug simulation.



Thanks and Regards
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[gmx-users] Error in installing Gromacs in Cygwin

[tasneem kausar]

Dear all
I have installed gromacs-5.1.2 in cygwin  64 bit computer. cmake have
finished successfully during installation. While executing  the command
"cygcheck /usr/local/gromacs/bin/pdb2gmx.exe" it gives following error-
cygcheck: track_down: could not find cyggmx-6.dll

cygcheck: track_down: could not find cyggmxpreprocess-6.dll

Kindly provide the  solution of this error.



Thanks and Regards
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[gmx-users] problem in editing .eps file of hbond

[tasneem kausar]

Dear all

I have plotted the hydrogen bonds present at the interface of protein in
its binary complex. I have already written the index file for the interface
residues then used it for hydrogen bond calculation. There are a number of
bonds at the interface. I am trying to put a cut off of 50 % for existence
of hydrogen bonds in the whole trajectroy. So I want to remove the rest of
hydrogen bonds of interface residues whose existence is less than 50% . For
this purpose how should I edit the .eps file. Because there are a lot of
data written and I am not able to understand the data that are given for x
and y axis.
Please solve the Issue

Thanks in advance
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[gmx-users] g_mmpbsa positive binding energy

[tasneem kausar]

Dear Gromacs Users
I am trying to calculate binding energy of protein-ligand and
protein-receptor complex using g_mmpbsa. I have run simulation of 10 ns and
snapshot was generated at every 1 ps. Initial 2ns was not taken. g_mmpbsa
was run for the rest of the frames. The command line was given as:
g_mmpbsa -f protein.xtc -s protein.tpr -n protein.ndx -dt 200 -b 2000 -e
1 -pdie 2
protein.ndx is index file of protein-ligand and protein-receptor.
 The binding energy with dielectric 2 comes out positive.  When I have
increased the dielectric, binding energy is still positive.
at dielectric 2  binding energy was 1028.010 kJ/mole
at dielectric 4  binding energy was 428.010 kJ/mole
at dielectric 8  binding energy was 128.015 kJ/mole
I have calculated the charge on the ligand and receptor using pdb2gmx. The
charge on the ligand protein is -12 and that of receptor protein is -5.
 How will I get the negative binding energy?
Any suggestion resolving this issue will be appreciated.


Thanks in Advance
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[gmx-users] vacuum simulation vs specific solvent simulation

[tasneem kausar]

Dear users

Dear gromacs users

As Joao replied and asked about the purpose of simulation.
I have performed the vacuum simulation.
I want to see the secondary structure change in vacuum and in specific
solvent.


mdp parameters are :.
;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  hbonds
integrator  = steep
nsteps  =  3000
;
;Energy minimizing stuff
;
emtol   =  2000
emstep  =  0.01

nstcomm =  1
ns_type =  simple
rlist   =  0.0
coulombtype =  cut-off
rcoulomb=  0.0
rvdw=  0.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl  =  no
Pcoupl  =  no
PBC =  no
gen_vel =  no


then i have run the full md for 5ns.
mdp parameter are as follows:

;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
constraints =  hbonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  250; total 5000 ps.
nstcomm =  1
nstxout =  50
nstvout =  50
comm-mode   =  ANGULAR
lincs_iter  =  2
nstfout =  0
nstlog  =  500
nstenergy   =  500
nstxtcout   =  500
xtc-precision   =  1000
nstlist =  10
ns_type =  simple
rlist   =  0.0
coulombtype =  cut-off
rcoulomb=  0.0
rvdw=  0.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =  no
tc-grps=  Protein
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  Protein
; Isotropic pressure coupling is now on
Pcoupl  =  no
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
PBC =  no


Am I using the correct mdp parameters for vacuum simulation.
If anyone know about this, please help...

Thanks and reagards
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 14

[tasneem kausar]

I want to see the change in secondary structure of the protein in vacuum as
well as in specific solvent.

On Wed, Sep 2, 2015 at 4:05 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
>
> Today's Topics:
>
>1. vacuum simulations (tasneem kausar)
>2. demux.pl input file (Nawel Mele)
>3. Re: trjconv -pbc nojump (Ganesh Shahane)
>4. Re: demux.pl input file (Andrea P?rez-Villa)
>5. Re: vacuum simulations (Jo?o Henriques)
>6. Re: demux.pl input file (Nawel Mele)
>
>
> ----------
>
> Message: 1
> Date: Wed, 2 Sep 2015 15:36:52 +0530
> From: tasneem kausar <tasneemkausa...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] vacuum simulations
> Message-ID:
> <
> cafak4ubfkk5m3b1bcwrngwg6_p3xgw5dzavr75liu1hl66+...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gromacs users
>
> I have performed the vacuum simulation of protein.
> The structure was minimized after generating the box using the following
> mdp parameters.
> ;
> ;User spoel (236)
> ;Wed Nov  3 17:12:44 1993
> ;Input file
> ;
> cpp =  /usr/bin/cpp
> define  =  -DFLEX_SPC
> constraints =  hbonds
> integrator  = steep
> nsteps  =  3000
> ;
> ;Energy minimizing stuff
> ;
> emtol   =  2000
> emstep  =  0.01
>
> nstcomm =  1
> ns_type =  simple
> rlist   =  0.0
> coulombtype =  cut-off
> rcoulomb=  0.0
> rvdw=  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl  =  no
> Pcoupl  =  no
> PBC =  no
> gen_vel =  no
>
>
> then i have run the full md for 5ns.
> mdp parameter are as follows:
>
> ;
> ;User spoel (236)
> ;Wed Nov  3 17:12:44 1993
> ;Input file
> ;
> title   =  Yo
> cpp =  /usr/bin/cpp
> constraints =  hbonds
> integrator  =  md
> dt  =  0.002; ps !
> nsteps  =  250; total 5000 ps.
> nstcomm =  1
> nstxout =  50
> nstvout =  50
> comm-mode   =  ANGULAR
> lincs_iter  =  2
> nstfout =  0
> nstlog  =  500
> nstenergy   =  500
> nstxtcout   =  500
> xtc-precision   =  1000
> nstlist =  10
> ns_type =  simple
> rlist   =  0.0
> coulombtype =  cut-off
> rcoulomb=  0.0
> rvdw=  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl  =  no
> tc-grps=  Protein
> tau_t   =  0.1
> ref_t   =  300
> ; Energy monitoring
> energygrps  =  Protein
> ; Isotropic pressure coupling is now on
> Pcoupl  =  no
> Pcoupltype  = isotropic
> tau_p   =  0.5
> compressibility =  4.5e-5
> ref_p   =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel =  yes
> gen_temp=  300.0
> gen_seed=  173529
> PBC =  no
>
>
> Is this a right way to perform the MD in vacuum?
> Anyone if familiar with this procedure, please suggest.
>
>
> Thanks in Advance
>
>
> --
>
> Message: 2
> Date: Wed, 2 Sep 2015 11:16:11 +0100
> From: Nawel Mele <nawel.m...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Subject: [gmx-users] demux.pl input file
> Message-ID:
> <
> cajtrp+o9qj0+6sjs73_doe9xuanrvcxmgeo1qkoctym2l5g...@mail.gmail.

[gmx-users] vacuum simulations

[tasneem kausar]

Dear gromacs users

I have performed the vacuum simulation of protein.
The structure was minimized after generating the box using the following
mdp parameters.
;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints =  hbonds
integrator  = steep
nsteps  =  3000
;
;Energy minimizing stuff
;
emtol   =  2000
emstep  =  0.01

nstcomm =  1
ns_type =  simple
rlist   =  0.0
coulombtype =  cut-off
rcoulomb=  0.0
rvdw=  0.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl  =  no
Pcoupl  =  no
PBC =  no
gen_vel =  no


then i have run the full md for 5ns.
mdp parameter are as follows:

;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
constraints =  hbonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  250; total 5000 ps.
nstcomm =  1
nstxout =  50
nstvout =  50
comm-mode   =  ANGULAR
lincs_iter  =  2
nstfout =  0
nstlog  =  500
nstenergy   =  500
nstxtcout   =  500
xtc-precision   =  1000
nstlist =  10
ns_type =  simple
rlist   =  0.0
coulombtype =  cut-off
rcoulomb=  0.0
rvdw=  0.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =  no
tc-grps=  Protein
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  Protein
; Isotropic pressure coupling is now on
Pcoupl  =  no
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
PBC =  no


Is this a right way to perform the MD in vacuum?
Anyone if familiar with this procedure, please suggest.


Thanks in Advance
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[gmx-users] vaccume simulation

[tasneem kausar]

Dear gmx-users
I am trying to calculate rmsd for protein backbone. I have done simulation
in vacuum. There are for negative charges in the system. During solvation
via genbox, 4 water molecule were added using -maxsol. The charges have
been neutralized by addition of 4 Na ion and water molecules were replaced
by these ions. Then after minimization I have run full md for 50 ns.

if there is any other way to neutralize the charge in vacuum, please tell.
Is the way I have opted for vavuum simulation right?

Any kind of help will be appreciated.

Thanks and Regards
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[gmx-users] forming disulfide linkage between two chains

[tasneem kausar]

sir

I am trying to make disulfide linkage between chain A and B.
The command line is pdb2gmx -f prtn.pdb -o prtn.gro -p prtn.top -ss.
I have used -ss option of pdb2gmx but disufide linkage is not formed
between the chains A and B.
What is the possible way to form the disulfide linkage in Gromacs usind the
pdb2gmx.
Please resolve the issue


Thanks in Advance
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[gmx-users] g_anaeig error

[tasneem kausar]

for PCA i used the g_covar followed by g_anaeig.
for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
these files are generated by g_covar.
g_anaeig gives the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 49

[tasneem kausar]

for PCA i used the g_covar followed by g_anaeig.
i used the command line for g_covr as
g_covar -f full.xtc -s full.tpr -o eig.xvg
I have selected the protein for least square fit and main chain for
covarience analysis.
There is a warning message.
WARNING: number of atoms in tpx (312) and trajectory (1061) do not match

The abve comman gave the files average.pdb, eigenvec.trr and eig.xvg
Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
The commnan line for g_anaeig is given below.
g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
For least square fit i have selected the protein and same for the
eigenvectors
This gave the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?

On Wed, Mar 11, 2015 at 3:31 PM, 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:

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 Today's Topics:

1. Binding free energy of an ion from alchemical transformation
   (Wojciech Kope?)
2. umbrella sampling tutorial (Ming Tang)
3. Re: enemat output (Mark Abraham)
4. g_anaeig error (tasneem kausar)
5. Thermostats and MSD (sujithkakkat .)
6. Re: g_anaeig error (Tsjerk Wassenaar)
7. Compiler (Alexander Tzanov)


 --

 Message: 1
 Date: Wed, 11 Mar 2015 09:23:53 +0100
 From: Wojciech Kope? 9000...@gmail.com
 To: gmx-us...@gromacs.org
 Subject: [gmx-users] Binding free energy of an ion from alchemical
 transformation
 Message-ID:
 
 cak_bonfb_m2mgxumw8gswhfzbtdifp4lkjw4pgbhvy3p5uc...@mail.gmail.com
 Content-Type: text/plain; charset=UTF-8

 Dear Gromacs users,

 I'm thinking about performing free energy calculations for a protein that
 binds cations,  using alchemical transformation method. In the simplest
 case I'd transform an ion (one atom) into a naked particle; however in this
 case I'd get a non-zero overall charge of the system during the charge
 decoupling. I'm aware of some corrections for that and also that Gromacs
 probably neutralises the charge with PME (?). Another approach I've been
 thinking of is to simultaneously couple a naked particle somewhere in the
 bulk with the environment, switching on the charge in a same way as the
 charge of the ion is being switched off. In this way, the charge would be 0
 all the time, and at the end of the simulation would yield the protein with
 an empty binding site and the ion somewhere in the bulk. Are there any
 obvious pitfalls with this approach?

 Thank you,
 Wojciech


 --

 Message: 2
 Date: Wed, 11 Mar 2015 08:17:42 +
 From: Ming Tang m21.t...@qut.edu.au
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 gromacs.org_gmx-users@maillist.sys.kth.se
 Subject: [gmx-users] umbrella sampling tutorial
 Message-ID:
 
 dm2pr0101mb10690504f9ed567db577b697b6...@dm2pr0101mb1069.prod.exchangelabs.com
 

 Content-Type: text/plain; charset=us-ascii

 Dear all,

 I was learning the Umbrella Sampling tutorial step by step on Gromacs
 5.0.4.
 Everything was fine until I got to the step five (run the continuous
 pulling simulation).
 Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
 failed.

 ; Pull code in tutorial
 pull= umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim= N N Y
 pull_start  = yes   ; define initial COM distance  0
 pull_ngroups= 1
 pull_group0 = Chain_B
 pull_group1 = Chain_A
 pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
 pull_k1 = 1000  ; kJ mol^-1 nm^-2

 ; COM pulling I modified
 pull= umbrella
 pull_geometry= distance  ; simple distance increase
 pull_dim = N N Y
 pull_start   = yes   ; define initial COM distance  0
 pull_coord1-groups   = 2
 pull-group1-name = Chain_B
 pull_group2-name = Chain_A
 pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
 pull-coord1-k= 1000  ; kJ mol^-1 nm^-2

 Fatal error:
 Group Chain_B referenced in the .mdp file was not found in the index file.
 Group names must match either [moleculetype] names or custom index group
 names, in which case you must supply an index file to the '-n' option
 of grompp.

 Index:
 [ r_1-27 ]
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