Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 40

[Farial Tavakoli]

ests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
> --
>
> Message: 4
> Date: Mon, 12 Nov 2018 19:01:29 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Group WAT referenced in the .mdp file was not
> found in the index file
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/12/18 7:14 AM, Rahma Dahmani wrote:
> > Hi GMX users,
> >
> > i double checked in my topology and gro files that i am using the same
> > moleculetype ( LIG and WAT) but when i run grompp for T equilibration i
> get
> > an error message """" Group WAT referenced in the .mdp file was not found
> > in the index file """"
> > PS: i am not using an index file  and i modified tc-grps, in nvt.mdp
> file ,
> > to :
> > tc-grps = LIG WAT .
> >
>
> The error means that "WAT" is not a valid group. What is it in your
> topology? The default water [moleculetype] in all GROMACS top
> <https://maps.google.com/?q=t+water+%5Bmoleculetype%5D+in+all+GROMACS+top=gmail=g>ologies
> is
> "SOL," not "WAT."
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
>
>
> --
>
> Message: 5
> Date: Mon, 12 Nov 2018 19:02:52 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] atomtype OV not found
> Message-ID: <10e914b3-e342-78e3-141e-7a541cc18...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/12/18 8:41 AM, Farial Tavakoli wrote:
> > Dear Mark
> >
> > I changed the way of topology generating in AMBER. The peptidic ligand
> (has
> > 2 phosphotyrosine residues) topology was generated using amber. all of
> the
> > files that I have in my working directory are, Leaprc.ff99SB,
> > Learc.phosaa10,  frcmod.phosaa10,  ligand.inpcrd,  ligand.prmtop.  The
> only
> > thing that I know to convert amber format to gromacs format is to use
> > acpype python script :
> > python acpype -p ligand.prmtop -x ligand.inpcrd
> > The .gro and .top files were generated. protein topology was generated
> > using amber99SB ff in gromacs and then complex.gro and .top files were
> > modified according to the tutorial in gromacs. But now, when I issue this
> > command:
> > gmx grompp -f .mdp -c .gro -p .top -o ions.tpr
> > I face to this error:
> > ERROR 1 [file mig_GMX.itp, line 60]:
> >Atomtype OV not found
> > OV atom is related to leaprc.phosaa10 file and I dont know what should I
> do
> > now?
> > I think , the leaprc.phosaa10 file has to be added to aminoacid.rtp file
> of
> > amber99SB.ff but I dont know how to convert it to gromacs format file?
> > Am I right?
> > WOuld you please guide me how to remove this Error?
>
> Your force field has to account for all the atom types required to run
> the simulation. You don't need to modify any .rtp files if you've
> already got a topology produced by other means. But that topology should
> be edited to introduce any new atom types required, associated bonded
> parameters, etc. When you do nonstandard things, you have to take
> nonstandard approaches...
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
>
>
> --
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 175, Issue 40
> **
>
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Re: [gmx-users] Lincs warning

[Farial Tavakoli]

Dear Mark

Thank you for your reply

I resolved my problem by refining the output ot the tool

Best
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[gmx-users] atomtype OV not found

[Farial Tavakoli]

Dear Mark

I changed the way of topology generating in AMBER. The peptidic ligand (has
2 phosphotyrosine residues) topology was generated using amber. all of the
files that I have in my working directory are, Leaprc.ff99SB,
Learc.phosaa10,  frcmod.phosaa10,  ligand.inpcrd,  ligand.prmtop.  The only
thing that I know to convert amber format to gromacs format is to use
acpype python script :
python acpype -p ligand.prmtop -x ligand.inpcrd
The .gro and .top files were generated. protein topology was generated
using amber99SB ff in gromacs and then complex.gro and .top files were
modified according to the tutorial in gromacs. But now, when I issue this
command:
gmx grompp -f .mdp -c .gro -p .top -o ions.tpr
I face to this error:
ERROR 1 [file mig_GMX.itp, line 60]:
  Atomtype OV not found
OV atom is related to leaprc.phosaa10 file and I dont know what should I do
now?
I think , the leaprc.phosaa10 file has to be added to aminoacid.rtp file of
amber99SB.ff but I dont know how to convert it to gromacs format file?
Am I right?
WOuld you please guide me how to remove this Error?

Best regards
Farial
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Re: [gmx-users] LINCS warning

[Farial Tavakoli]

Dear Mark

Thank you for your reply
I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this
results:
EM results:

Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -3.4145945e+03
Maximum force =  6.6494578e+04 on atom 81
Norm of force =  1.0602226e+04

and NVT results:

starting mdrun 'mig'
20 steps, 10.0 ps.
step 199900, remaining wall clock time: 0 s
Writing final coordinates.
step 20, remaining wall clock time: 0 s
   Core t (s)   Wall t (s)(%)
   Time:  349.726   87.431  400.0
 (ns/day)(hour/ns)
Performance:9.8822.429
I checked ligand.gro (generated using acpype script) and nvt.gro (generated
by dt = 0.5) files by VMD and noticed the phosphate groups were not
bound to tyrosine residues in ligand.gro and there was bad contacts in them
in nvt.gro . Is it because of VMD software or there is a problem in
converting files?
If it is needed I will send you my files to you.

Thanks in advance
Farial
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[gmx-users] LINCS warning

[Farial Tavakoli]

Dear gromacs users

I am trying to simulate a complex, including a protein and a peptidec
ligand with 2 phosphotyrosine residues.
The protein topology was generated using amber99sb.ff in gromacs and the
ligand topology was generated using ff99sb in amber tools 16, then the
.inpcrd and .prmtop files were converted to .gmx and .top files using
acpype python script.
*python acpype.py -p prmtop -x inpcrd*
.itp file was created by removing  header and footer of .top file.
Then .gro and .top files were modified according to the tutorial in
gromacs.
I tryed to minimize the complex , but it stoped before 100 steps :





*Steepest Descents converged to machine precision in 80 steps,but did not
reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
force =  7.0647156e+04 on atom 5256Norm of force =  5.8775842e+02*

and when I run NVT simulation , faced to LINCS warning:










*starting mdrun 'Protein in water'20 steps,400.0 ps.step 0Step 5,
time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
length   5258   5261   90.00.0960   0.1665  0.0960   5283   5286
90.00.0960   0.1425  0.0960Wrote pdb files with previous and
current coordinates*
I separated my complex in to protein and ligand and simulated the protein
alone in the TIP3P water model. that was stable. then, simulated the ligand
in vacuo and faced with LINCS warning.
Both force fields that were used to generate topologies were AMBER99sb, Is
it possible its because of .mdp files which I used?
Would you please reply and advice me how I can resolve this problem?

best regards
Farial

the em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
cutoff-scheme   = Verlet
ns_type = grid
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.0
pbc = xyz

nvt.mdp file:
title   = AMBER  NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md
nsteps  = 20 ; 2 * 20 = 400 ps
dt  = 0.002
; Output control
nstxout = 500
nstvout = 500
nstenergy   = 500
nstlog  = 500
; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order = 4
; Nonbonded settings
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 10
rcoulomb= 1.0
rvdw= 1.0
; Electrostatics
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16
; Temperature coupling is on
tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300
; Pressure coupling is off
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
; Velocity generation
gen_vel = yes
gen_temp= 300
gen_seed= -1
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Re: [gmx-users] DispErsion correction

[Farial Tavakoli]

Dear Justin and Dallas

Thank you for your replying

I have another problem in minimizing and NVT run of my complex, including a
protein and a peptidic ligand which the ligand has 2 phosphotyrosine
residues. I generated a topology file of ligand using ff14sb in ambertools
16 and then converted the .inpcrd and .prmtop files in .gro and .top files
using acpype python script. The protein topology was generated using
amber99sb ff in GROMACS.
Then, I cited to gromacs manuscript in order to generate an .itp file of
ligand from .top file and generated .itp file by removing the header and
footer of .top file in such a way that .itp file starts with :
[ moleculetype ]
;namenrexcl
 mig   3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 1   N3 1   THR N1 0.181200 14.01000 ; qtot 0.181
 2H 1   THRH12 0.193400  1.00800 ; qtot 0.375
.
.
.
and ends with
120123122132  1   180.00   4.18400   2 ;  C-
CD- N-CA
   132135134136  1   180.00  43.93200   2 ; CA-
O- C-   OXT
then, modified the complex.gro and .top files according to the tutorials in
gromacs, I Minimized the complex by issuing this coomand:
gmx grompp -f em.mdp -c solv-ions.gro -p topol.top -o em.tpr
gmx mdrun -v -defnm em
but noticed that the minimization ended soon :

Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -6.5639856e+05
Maximum force =  7.0647156e+04 on atom 5256
Norm of force =  5.8775842e+02

and when performed the NVT run , faced to this error:

starting mdrun 'Protein in water'
20 steps,400.0 ps.
step 0
Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016999, max 0.734404 (between atoms 5258 and 5261)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5258   5261   90.00.0960   0.1665  0.0960
   5283   5286   90.00.0960   0.1425  0.0960
Wrote pdb files with previous and current coordinates
.
.
.
It should be noted that atoms 5258 and 5261 are related to sol molecules.
TIP3P water model was selected for amber99sb force field.
Would you please advice and guild me how should I resolve this problem?

Thanks in advance
Farial


these are the .mdp files that I used:
em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Minimization step size
nsteps  = 5 ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
cutoff-scheme   = Verlet; Buffered neighbor searching
ns_type = grid  ; Method to determine neighbor list (simple,
grid)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions in all 3
dimensions


the nvt.mdp file:
title   = AMBER  NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 20 ; 2 * 20 = 400 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = h-bonds   ; bonds involving H are constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme   = Verlet; Buffered neighbor searching
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff (in
nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 

[gmx-users] DispErsion correction

[Farial Tavakoli]

Dear gmx users

I am trying to simulate my complex using amber99sb ff. There is no amber
tutorial in gromacs. I need to know how dispersion correction set in the
.mdp files . I can not understand the definitions of DispCorr in mdp
option. Should I put it on EnerPres or no ?
Would you please clarify me and explain it in short?

Thanks in advance
Farial
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[gmx-users] acpype is not working

[Farial Tavakoli]

Dear all

I am trying to convert .oFF and .FRCMOD format files to the format that is
compatible with GMX format, so I installed anaconda to use conda install -c
acpype -c openbabel -c ambermd command because I did not install amber and
openbabel programs. then issued this command:
conda install -c acpype -c openbabel -c ambermd python=3.7
and the system replied:
solving environment: done
All requested packages already installed.
But now when I issue the command:
"acpype -h or antechamber -h" in the terminal, face to this error:
acpype: command not found
antechamber: command not found
Is there anyone who can help me to solve the problem?
I would be appreciated it if anyone can help me.

Thanks in advance
Farial
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[gmx-users] Acpype and antechamber

[Farial Tavakoli]

Hi Bhupendra

Thank you for your reply
You asked me yesterday “Are you on line now? “ and I replied “ yes I am on
line “
Anyway, I issued this command :
" conda install -c acpype -c openbabel -c antechambermd python=3.7
and the system replied :
"Solving environment: done
# All requested packages already installed."
but now when I type " acpype -h or antechamber -h" in my terminal , face to
this error:
acpype: command not found
antechamber: command not found
Shoul I go to the special directory?
Would you please help me to solve the problem?

Thanks in advance
Farial
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 71

[Farial Tavakoli]

Hi Bhupendra

yes i am on lone now.

Farial

On Mon, Oct 29, 2018 at 2:11 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. Error of CgenFF convert to itp (Mijiddorj B)
>2. acpype and conda (Farial Tavakoli)
>3. Re: acpype and conda (Bhupendra Dandekar)
>4. Place a gap in y-axis (Raag Saluja)
>5. Selection of residues in one of the chains of heterodimer
>   (Raag Saluja)
>6. Temperature in CG production runs (Yasser Almeida Hern?ndez)
>
>
> --
>
> Message: 1
> Date: Mon, 29 Oct 2018 12:04:48 +0900
> From: Mijiddorj B 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Error of CgenFF convert to itp
> Message-ID:
> <
> cabgrapugyqmdqtsaxd-xomwrvfhazquwgkltxpejcx3fomg...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I would like to generate parameters for small molecule using CGenFF. I
> generated str file using cgenFF. However, I could not convert to itp file
> using cgenff_charmm2gmx.py because of following error:
> Please advice me.
>
> NOTE2: Please be sure to use the same version of CGenFF in your simulations
> that was used during parameter generation:
> --Version of CGenFF detected in  mol.str : 4.0
> --Version of CGenFF detected in  charmm36.ff/forcefield.doc : 4.0
>
> NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
> parameters that are already in CGenFF' option when uploading a molecule
> into CGenFF.
> Traceback (most recent call last):
>   File "./cgenff_charmm2gmx.py", line 799, in 
> m.read_charmm_rtp(rtplines,atomtypes)
>   File "./cgenff_charmm2gmx.py", line 540, in read_charmm_rtp
> self.G.add_node(self.natoms, atm[self.natoms])
> TypeError: add_node() takes exactly 2 arguments (3 given)
>
>
> --
>
> Message: 2
> Date: Mon, 29 Oct 2018 10:09:41 +0330
> From: Farial Tavakoli 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] acpype and conda
> Message-ID:
> <
> cadmafqeu45d30nk734ffij4nexnyfr5d8ngjrmrfsigovsm...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
>  Dear Bhupendra
>
> Thanks for your reply
>
> I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> -h or acpype.py -h , but face with this error:
> acpype: command not found
> I can run acpype only when type python command before it.
> In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on "/home/vaio"
> yesterday and issued the "conda install -c acpype -c openbabel -c ambermd"
> command
> but faced with this error:
>  CondaValueError: too few arguments, must supply command line package specs
>  or --file
>  python version = python 2.7.15
> Would you please help me ? I dont know how I should deal with these
> problems.
>
> Thanks in advance
> Farial
>
>
> ------
>
> Message: 3
> Date: Mon, 29 Oct 2018 12:26:26 +0530
> From: Bhupendra Dandekar 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] acpype and conda
> Message-ID:
>  mk1mb-d...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Farial,
> Are you online now?
>
> Bhupendra
>
> On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli <
> faryal.tavak...@gmail.com>
> wrote:
>
> >  Dear Bhupendra
> >
> > Thanks for your reply
> >
> > I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> > -h or acpype.py -h , but face with this error:
> > acpype: command not found
> > I can run acpype only when type python command before it.
> > In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on "/home/vaio"
> > yesterday and issued the "conda install -c acpype -c openbabel -c
> ambermd"
> > command
> > but faced with this error:
> >  CondaValueError: too few arg

[gmx-users] acpype and conda

[Farial Tavakoli]

 Dear Bhupendra

Thanks for your reply

I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
-h or acpype.py -h , but face with this error:
acpype: command not found
I can run acpype only when type python command before it.
In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on "/home/vaio"
yesterday and issued the "conda install -c acpype -c openbabel -c ambermd"
command
but faced with this error:
 CondaValueError: too few arguments, must supply command line package specs
 or --file
 python version = python 2.7.15
Would you please help me ? I dont know how I should deal with these
problems.

Thanks in advance
Farial
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 62

[Farial Tavakoli]

bhupendra.dandekar...@gmail.com> wrote:
> > >
> > > > I actually got lot of help from Luciano Kagami about installation and
> > > usage
> > > > of acpype and ligro.
> > > > Thanks to both of you.
> > > >
> > > > Bhupendra
> > > >
> > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > > > bhupendra.dandekar...@gmail.com> wrote:
> > > >
> > > > > Thanks to you also sir.
> > > > > Your work is really appreciated and is really helpful.
> > > > >
> > > > >
> > > > > Bhupendra
> > > > >
> > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
> > > > >
> > > > >> Thanks Bhupendra, indeed we have this option, which is
> experimental,
> > > but
> > > > >> I'm glad to see some are already using it and it seems to be
> > working.
> > > > >>
> > > > >> Alan
> > > > >>
> > > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > > > >> bhupendra.dandekar...@gmail.com> wrote:
> > > > >>
> > > > >> > Dear Farial,
> > > > >> >
> > > > >> > Use this command to install acpype and antechamber using conda:
> > > > >> >
> > > > >> > conda install -c acpype -c openbabel -c ambermd
> > > > >> >
> > > > >> > and then you can check and call acpype, antechamber like this
> from
> > > > your
> > > > >> > terminal:
> > > > >> >
> > > > >> > acpype -h
> > > > >> > antechamber -h
> > > > >> >
> > > > >> > then you can generate ligand topology using this command:
> > > > >> >
> > > > >> > acpype -i FFF.pdb -b FFF -o gmx
> > > > >> >
> > > > >> > Hope this helps. Let me know if you have any questions.
> > > > >> >
> > > > >> > Thanks
> > > > >> > Bhupendra
> > > > >> >
> > > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> > > > >> faryal.tavak...@gmail.com
> > > > >> > >
> > > > >> > wrote:
> > > > >> >
> > > > >> > > Dear GMX useres
> > > > >> > >
> > > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from
> > AMBER
> > > > >> > parameter
> > > > >> > > database (Bryce Group: Computational Biophysics and Drug
> Design
> > -
> > > > >> > > University of Manchester)
> > > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the
> > > format
> > > > >> that
> > > > >> > > GROMACS is compatible with in .rtp files*. so referred to
> > GROMACS
> > > > >> > tutorial
> > > > >> > > protein-ligand complex and downloaded acpype. installed it
> using
> > > its
> > > > >> > > readme.txt file but whenever i typed../acpype.py -i
> FFF.pdb
> > >  At
> > > > >> > folder
> > > > >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > > > >> > >
> > > > >> > >
> > > > >> > > *bash: ../acpype.py: No such file or directory*
> > > > >> > >
> > > > >> > > *while when I typed whereis acpype in terminal , the operating
> > > > system
> > > > >> > says
> > > > >> > > :*
> > > > >> > >
> > > > >> > >
> > > > >> > > *acpype: /usr/local/bin/acpype*
> > > > >> > > * it means there is the executable file of acpype . so how
> come
> > I
> > > > type
> > > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO
> > such
> > > > >> file or
> > > > >> > > directory?*
> > > > >> > > *Is there anyone who ca help me?*
> > > > >> > > *I rea

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 61

[Farial Tavakoli]

Dear Bhupendra

Thank you for your replying.

I typed the same command that you said: conda install -c acpype -c
openbabel -c ambermd
but the system said :
conda: command not found
or but when I typed : "python acpype.py -i XXX.pdb -b XXX -o gmx" or
"python acpype.py -i XXX.mol2 -o gmx" faced to this error:
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2018 AWSdS |

ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second
 I would be appreciated it if you can help me

Best regards
Farial

On Wed, Oct 24, 2018 at 10:17 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: acpype (neelam wafa)
>2. Simulated tempering (Gregory Man Kai Poon)
>3. Re: parameters for plotting 2D density map with gmx densmap
>   and xpm2ps (Wenjuan Jiang)
>4. Re: Adding residue to .rtp file (Raji)
>
>
> --
>
> Message: 1
> Date: Wed, 24 Oct 2018 20:57:45 +0500
> From: neelam wafa 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] acpype
> Message-ID:
>  ou0-y...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi alan
>
> Can you please tell how long will it take for the online acpype server to
> be available?
>
> Regards
> Neelam wafa
>
> On Wed, 24 Oct 2018, 6:23 pm Alan,  wrote:
>
> > Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> > will have more things to show eventually.
> >
> > Alan
> >
> > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> > bhupendra.dandekar...@gmail.com> wrote:
> >
> > > I actually got lot of help from Luciano Kagami about installation and
> > usage
> > > of acpype and ligro.
> > > Thanks to both of you.
> > >
> > > Bhupendra
> > >
> > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > > bhupendra.dandekar...@gmail.com> wrote:
> > >
> > > > Thanks to you also sir.
> > > > Your work is really appreciated and is really helpful.
> > > >
> > > >
> > > > Bhupendra
> > > >
> > > > On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
> > > >
> > > >> Thanks Bhupendra, indeed we have this option, which is experimental,
> > but
> > > >> I'm glad to see some are already using it and it seems to be
> working.
> > > >>
> > > >> Alan
> > > >>
> > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > > >> bhupendra.dandekar...@gmail.com> wrote:
> > > >>
> > > >> > Dear Farial,
> > > >> >
> > > >> > Use this command to install acpype and antechamber using conda:
> > > >> >
> > > >> > conda install -c acpype -c openbabel -c ambermd
> > > >> >
> > > >> > and then you can check and call acpype, antechamber like this from
> > > your
> > > >> > terminal:
> > > >> >
> > > >> > acpype -h
> > > >> > antechamber -h
> > > >> >
> > > >> > then you can generate ligand topology using this command:
> > > >> >
> > > >> > acpype -i FFF.pdb -b FFF -o gmx
> > > >> >
> > > >> > Hope this helps. Let me know if you have any questions.
> > > >> >
> > > >> > Thanks
> > > >> > Bhupendra
> > > >> >
> > > >> > On Wed, Oct 24, 20

[gmx-users] acpype

[farial tavakoli]

Dear Justin
I installed acpype on the ubuntu but didnt install Antechamber and openbable . 
Now I am trying to convert the AMBER parameters format (obtained from 
http://sites.pharmacy.manchester.ac.uk/bryce/amber  ) to the one that gromacs 
is compatible with in the .rtp files. I pasted acpype.py in the directory that 
I am working and issued this command:
python acpype.py -i XXX.pdb 
but faced to this error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting ! 
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
    What 'which antechamber' in your terminal says?
    'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

while I read in the readme.txt file of acpype and in google that ' However, if 
one wants *acpype* just to emulate *amb2gmx.pl*, one needs nothing at all but 
*[http://www.python.org Python]*.'  or  'ACPYPE is far better than amb2gmx.pl 
and won't even need AmberTools if you
just want to covert Amber topology to GMX'.
 I can not understand where the problem is? 
I would be appreciated it if you help me
thanks in advanceFarial

 


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[gmx-users] acpype

[Farial Tavakoli]

Dear GMX useres

I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter
database (Bryce Group: Computational Biophysics and Drug Design -
University of Manchester)
 to the format that
GROMACS is compatible with in .rtp files*. so referred to GROMACS tutorial
protein-ligand complex and downloaded acpype. installed it using its
readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At folder
*acpype/test*   (/Downloads/acpype-master/acpype) or
(/Downloads/acpype-master/acpype/test) faced to this error:*


*bash: ../acpype.py: No such file or directory*

*while when I typed whereis acpype in terminal , the operating system says
:*


*acpype: /usr/local/bin/acpype*
* it means there is the executable file of acpype . so how come I type
../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
directory?*
*Is there anyone who ca help me?*
*I really would be appreciated it if one help me to solve this and can
convert the AMBER format files to GRMACS format files.*

*best regards*
*Farial*
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[gmx-users] acpype

[farial tavakoli]

Dear GMX useres
I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter 
database (Bryce Group: Computational Biophysics and Drug Design - University of 
Manchester) to the format that GROMACS is compatible with in .rtp files. so 
referred to GROMACS tutorial protein-ligand complex and downloaded acpype. 
installed it using its readme.txt file but whenever i typed    ../acpype.py -i 
FFF.pdb   At folder *acpype/test*   (/Downloads/acpype-master/acpype) or    
(/Downloads/acpype-master/acpype/test) faced to this error:
bash: ../acpype.py: No such file or directory

while when I typed whereis acpype in terminal , the operating system says 
:acpype: /usr/local/bin/acpype

 it means there is the executable file of acpype . so how come I type  
../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or 
directory?Is there anyone who ca help me?I really would be appreciated it if 
one help me to solve this and can convert the AMBER format files to GRMACS 
format files.
best regardsFarial
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[gmx-users] phosphorylated residues simulation usinh gromacs

[farial tavakoli]

Dear GMX users
I need to simulate the complex composed of a protein and a peptide which has 
phosphotyrosine using AMBER99SB force field in GROMACS. cited to the " 
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/index.html " 
to download .OFF and .FRCMOD files of phosphotyrosine. but now I dont know how 
to use these files in GROMACS. There is no AMBER tutorial in gromacs . I 
searched google to find that but couldnt find stage by stage guides. Is there 
anyone can help me how I should use these files in GROMACS?I am sorry because 
of my english.
Thanks in advanceFarial
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Re: [gmx-users] energy minimization

[farial tavakoli]

Dear Justin 

I used LigParGen server to generate ligand topology but I dont know what 
changes I have to do in .itp file. 
 when I issued this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor 

faced this error:ERROR 1 [file LIG.itp, line 11]:
  Atomtype opls_800 not found
I checked the aminoacids.rtp file  of  
/usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype 
opls_800 and 801 and ... in this file. while the LIG.itp which generated by 
LigParGen server has atomtype opls_800 , 801 and ... . 
I have to modify all of these atomtype opls_ in order to correspond to with 
aminoacid.rtp file? 
I would be thankfull if you help me.
bestFraial


   On Monday, July 16, 2018, 5:29:17 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/16/18 3:49 AM, farial tavakoli wrote:
>  Dear Justin
>
> Thank you for your reply
> I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
> named topologen_1.1.pl in the working directory)
> I generated my ligand topology but got this :
> No output type specified. Using default type of .top
> Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
> Using default H type for atom 16.
> Using default H type for atom 26.
> Using default H type for atom 31.
> Using default H type for atom 38.
> Using default H type for atom 39.
> Using default H type for atom 40.
> Using default H type for atom 41.
> Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
> Using default H type for atom 47.
> Using default H type for atom 48.
> Using default H type for atom 49.
> Using default H type for atom 50.
> Using default H type for atom 51.
> Using default H type for atom 52.
>
> 
> WARNING: Net charge on the molecule is -2.781
> You will need to make corrections to the output topology
> 
>
> TopolGen, version 1.1_dev (10/14/2009) complete.
>
> Output topology has been written. An attempt has been made to assign charges 
> and atom types based
> on existing functional groups, but they may not be correct.  No charge 
> calculations or other
> parameterization calculations have been done.  Guesses have been made for 
> charge groups.  Please
> inspect and correct the topology before using it in any simulations.  The 
> author of the script does
> NOT guarantee accuracy or usability of any of the content; TopolGen was 
> written as a convenience
> for outputting a skeleton topology, and nothing more.

Heed the above warning. TopolGen assigns parameters based on similarity 
to known functional groups. If your molecule has something unusual, it 
makes no attempt to try to assign reasonable parameters. You'll need to 
actually parametrize the molecule. Make use of available web servers 
like LikeParGen or others.

-Justin

>
> the N13 atom connected to C with double bond. it sounds topolgen can not 
> identify N atom in 2 bonds with C .
> would you please help me to figure out this problem
> thans in advanceFarial
>
>      On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
> wrote:
>  
>  
>
> On 7/15/18 1:38 AM, farial tavakoli wrote:
>>    Dear Justin
>>
>> But I copied & pasted topolgen and perl5 folders in the working directory. 
>> and faced the mentioned error.
>>
>> Can't open perl script "topolgen.pl": No such file or directory
>> I dont know how I should figure out this problem.
> The problem is still the same: there's nothing called "topolgen.pl" in
> the working directory. List your files, you'll see it's called something
> else.
>
>> Which one of all-atom force fields will you choose to run a simulation on a 
>> complex with small molecule, if you want to calculate binding energy using 
>> G_MMPBSA ?I really need your guidance .
> Presumably any of them, but I don't do such calculations.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] make index

[farial tavakoli]

Dear GMX users
I am trying to make an index.ndx file of my complex which includes a receptor 
and a peptide using this command:

  gmx make_ndx -f em.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   330    Protein residues
There are: 15278  Water residues
There are: 7    Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...

  0 System  : 51172 atoms
  1 Protein :  5331 atoms
  2 Protein-H   :  2659 atoms
  3 C-alpha :   330 atoms
  4 Backbone    :   990 atoms
  5 MainChain   :  1322 atoms
  6 MainChain+Cb    :  1633 atoms
  7 MainChain+H :  1639 atoms
  8 SideChain   :  3692 atoms
  9 SideChain-H :  1337 atoms
 10 Prot-Masses :  5331 atoms
 11 non-Protein : 45841 atoms
 12 Water   : 45834 atoms
 13 SOL : 45834 atoms
 14 non-Water   :  5338 atoms
 15 Ion : 7 atoms
 16 NA  : 7 atoms
 17 Water_and_ions  : 45841 atoms

 nr : group  '!': not  'name' nr name   'splitch' nr    Enter: list groups
 'a': atom   '&': and  'del' nr 'splitres' nr   'l': list residues
 't': atom type  '|': or   'keep' nr    'splitat' nr    'h': help
 'r': residue  'res' nr 'chain' char
 "name": group 'case': case sensitive   'q': save and quit
 'ri': residue index

> splitch 1

Found 10 chains
1:   189 atoms (1 to 189)
2:   108 atoms (190 to 297)
3:   283 atoms (298 to 580)
4:   130 atoms (581 to 710)
5:   173 atoms (711 to 883)
6:    10 atoms (884 to 893)
7:  4087 atoms (894 to 4980)
8:    99 atoms (4981 to 5079)
9:   125 atoms (5080 to 5204)
10:   127 atoms (5205 to 5331)
I dont know it found 10 chains instead of finding 2 chains ( chain A and chain 
B).How can I make the desired index file composed of:18 protein chain A19 
protein chain B

best regardsFarial
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Re: [gmx-users] energy minimization

[farial tavakoli]

 Dear Justin 

Thank you for your reply
I noticed my problem ( the reason was topolgen.pl name in my directory, it is 
named topologen_1.1.pl in the working directory) 
I generated my ligand topology but got this :
No output type specified. Using default type of .top
Unknown atom type: N 13 with 2 bonds - cannot assign atom type.
Using default H type for atom 16.
Using default H type for atom 26.
Using default H type for atom 31.
Using default H type for atom 38.
Using default H type for atom 39.
Using default H type for atom 40.
Using default H type for atom 41.
Unknown atom type: N 42 with 2 bonds - cannot assign atom type.
Using default H type for atom 47.
Using default H type for atom 48.
Using default H type for atom 49.
Using default H type for atom 50.
Using default H type for atom 51.
Using default H type for atom 52.


WARNING: Net charge on the molecule is -2.781
You will need to make corrections to the output topology


TopolGen, version 1.1_dev (10/14/2009) complete.

Output topology has been written. An attempt has been made to assign charges 
and atom types based
on existing functional groups, but they may not be correct.  No charge 
calculations or other 
parameterization calculations have been done.  Guesses have been made for 
charge groups.  Please
inspect and correct the topology before using it in any simulations.  The 
author of the script does 
NOT guarantee accuracy or usability of any of the content; TopolGen was written 
as a convenience 
for outputting a skeleton topology, and nothing more.


the N13 atom connected to C with double bond. it sounds topolgen can not 
identify N atom in 2 bonds with C . 
would you please help me to figure out this problem
thans in advanceFarial

On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/15/18 1:38 AM, farial tavakoli wrote:
>  Dear Justin
>
> But I copied & pasted topolgen and perl5 folders in the working directory. 
> and faced the mentioned error.
>
> Can't open perl script "topolgen.pl": No such file or directory
> I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in 
the working directory. List your files, you'll see it's called something 
else.

> Which one of all-atom force fields will you choose to run a simulation on a 
> complex with small molecule, if you want to calculate binding energy using 
> G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[farial tavakoli]

 Dear Justin 

But I copied & pasted topolgen and perl5 folders in the working directory. and 
faced the mentioned error. 

Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem. 
Which one of all-atom force fields will you choose to run a simulation on a 
complex with small molecule, if you want to calculate binding energy using 
G_MMPBSA ?I really need your guidance .
best 
Farial
On Saturday, July 14, 2018, 6:35:27 PM GMT+4:30, Justin Lemkul 
 wrote:  
 
 

On 7/14/18 5:03 AM, farial tavakoli wrote:
>  
> Dear justin
>
> I am trying to run a simulation on my complex which has small molecule as a 
> ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then 
> installed perl script on linux. then typed "perl -v" to check if it is 
> installed. the perl 5.20.1 was installed.
> but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type 
> itp/top] " command to generate ligand topology , faced with this error:
> Can't open perl script "topolgen.pl": No such file or directory
> Infact I am new user in generation topology for small molecules using OPLSAA 
> ff. Would you please  help me to figure out this problem?

"No such file or directory" means the file isn't in the working 
directory. This is a generic error message from your shell and nothing 
specific about the script itself.

-Justin
>
> Farial
> best
>      On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
> wrote:
>  
>  
>
> On 2/20/18 12:52 PM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Dear Justin
>> Thank you for the reply
>> You meant , to tweak the emtol doesn't have noticable affects on the 
>> conformational enssemble generated by MD?
>>    
> Precisely what I said, yes.
>
> -Justin
>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  
>> wrote:
>>
>>
>>
>> On 2/20/18 4:52 AM, farial tavakoli wrote:
>>> Dear GMX users
>>> I used CHARMM36 all atom force field to generate .top and .gro files for my 
>>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
>>> residues, then ran a md simulation on it and then used g_mmpbsa to 
>>> calculate the binding free energy by pdies ( 2 and 4) but got + 426 and 
>>> +527 kjol/mol, respectively. While, I calculated binding energy before for 
>>> many other complexes without any phosphate groups using OPLS all atom force 
>>> field and pdie = 2 and obtained minus energy. But this time , I dont know 
>>> why I got positive binding energy? Is it because of charmm36 all atom force 
>>> field , the phosphate groups or it is needed to be energy minimized under 
>>> more restriction situations?
>>> I am checking different factors to understand its reason, so I wanted to 
>>> know , would it be ok if I energy minimize the complex with more 
>>> restriction situations ? for example by specifying emtol under 1000 
>>> kj/mol/nm , like 800 ? I think the positive binding energy might be because 
>>> of the complex didnt minimized well. however I checked the em.log file and 
>>> saw it was minimized well:
>>>
>>> Steepest Descents converged to Fmax < 1000 in 241 steps
>>> Potential Energy  = -6.5047744e+05
>>> Maximum force =  9.8285083e+02 on atom 3335
>>> Norm of force =  3.6905827e+01
>>> Is there anyone can advice me in energy minimization with emtol 800?
>> The purpose of energy minimization is to establish a reasonable starting
>> point for your simulation. Tweaks to emtol will have little to no
>> noticeable bearing on the conformational ensemble generated by MD.
>>
>> -Justin
>>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] topolgen

[farial tavakoli]

Dear gromacs users
I am trying to run a simulation on my complex which has small molecule as a 
ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then 
installed perl script on linux. then typed "perl -v" to check if it is 
installed. the perl 5.20.1 is installed. 
but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] 
" command to generate ligand topology , faced with this error:
Can't open perl script "topolgen.pl": No such file or directory
Is there anyone to  help me to figure out this problem? 
Infact I am new user in generation topology for small molecules using OPLSAA 
ff. 

best 
Farial
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[gmx-users] ligpargen

[farial tavakoli]

Dear GROMACS users
I am trying to run an md simulation on my protein in complex to a small 
molecule, using OPLSAA force field. then I am going to calculate binding energy 
using G_MMPBSA, G_MMPBSA is not able to calculate the binding energy with 
CHARMM36 force field, so I have to use OPLSAA. 
which one of topolbuild, topolgen and ligpargen programs is advised to generate 
topology for my small molecule?
best regards
Farial
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[gmx-users] phosphotyrosine peptide

[farial tavakoli]

Dear GMX users
I performed a simulation on the complex composed of a protein and a peptide 
which has 2 residues phosphotyrosines using charmm36 force field in GROMACS. 
After that I used g_mmpbsa to calculate the binding energy and energy 
contribution per residue , but the binding energy was calculated + 426 kj/mol. 
I sent an email to gmmbsa mailing list and informed them , but they replied :"  
we have not tested the g_mmpbsa with charmm36 so we can't say about the 
validity. Other members of g_mmpbsa tool, also previously reported about the 
positive binding energy when using charmm36 force field." in fact they couldnt 
help me. as they noticed , it is because of using charmm36 ff. Is there anyone 
can help me which force field I should use in gromacs till I wont have any 
problem when I am going to use g-mmpbsa ? 
best regardsFarial
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Re: [gmx-users] energy minimization

[farial tavakoli]

Dear Justin
In according to obtaining positive binding free energy using g_mmpbsa for my 
complex which has 2 phosphotyrosine residues and is simulated by charmm36 force 
field , I sent an email to g_mmpbsa mailing list and informed them to help me 
for solving my problem, but they replied me : " we have not tested the g_mmpbsa 
with charmm36 so we can't say about the validity. Other members of g_mmpbsa 
tool, also previously reported about the positive binding energy when using 
charmm36 force field." I sent another email to them :would you please advice me 
how could I calculate the  free binding energy of my complex (receptor and 
ligand that has 2 phosphotyrosine residues ) which has been simulated by 
charmm36 all atom force field? but I have not any response yet.
 so I decided to use a modified amber99s force field to use in gromacs to 
simulate my complex. and then use g_mmpbsa to calculate the binding energy. I 
searched the net and found this one to modify the amber99s ff : 
http://www.pharmacy.manchester.ac.uk/bryce/amberbut it is not for gromacs. 
Would you please advice me how can I get a modified amber force field to 
simulate my complex using gromacs?or help me how  can I calcualte the binding 
energy of my complex which is simulated by charmm36 in gromacs?
with best regardsFarial
 

On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 2/20/18 12:52 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear Justin
> Thank you for the reply
> You meant , to tweak the emtol doesn't have noticable affects on the 
> conformational enssemble generated by MD?
>  

Precisely what I said, yes.

-Justin

>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
> On 2/20/18 4:52 AM, farial tavakoli wrote:
>> Dear GMX users
>> I used CHARMM36 all atom force field to generate .top and .gro files for my 
>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
>> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
>> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
>> respectively. While, I calculated binding energy before for many other 
>> complexes without any phosphate groups using OPLS all atom force field and 
>> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
>> positive binding energy? Is it because of charmm36 all atom force field , 
>> the phosphate groups or it is needed to be energy minimized under more 
>> restriction situations?
>> I am checking different factors to understand its reason, so I wanted to 
>> know , would it be ok if I energy minimize the complex with more restriction 
>> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
>> ? I think the positive binding energy might be because of the complex didnt 
>> minimized well. however I checked the em.log file and saw it was minimized 
>> well:
>>
>> Steepest Descents converged to Fmax < 1000 in 241 steps
>> Potential Energy  = -6.5047744e+05
>> Maximum force =  9.8285083e+02 on atom 3335
>> Norm of force =  3.6905827e+01
>> Is there anyone can advice me in energy minimization with emtol 800?
> The purpose of energy minimization is to establish a reasonable starting
> point for your simulation. Tweaks to emtol will have little to no
> noticeable bearing on the conformational ensemble generated by MD.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] energy minimization

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD? 
 

Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:
> Dear GMX users
> I used CHARMM36 all atom force field to generate .top and .gro files for my 
> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
> respectively. While, I calculated binding energy before for many other 
> complexes without any phosphate groups using OPLS all atom force field and 
> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
> positive binding energy? Is it because of charmm36 all atom force field , the 
> phosphate groups or it is needed to be energy minimized under more 
> restriction situations?
> I am checking different factors to understand its reason, so I wanted to know 
> , would it be ok if I energy minimize the complex with more restriction 
> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
> ? I think the positive binding energy might be because of the complex didnt 
> minimized well. however I checked the em.log file and saw it was minimized 
> well:
>
> Steepest Descents converged to Fmax < 1000 in 241 steps
> Potential Energy  = -6.5047744e+05
> Maximum force =  9.8285083e+02 on atom 3335
> Norm of force =  3.6905827e+01
> Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] energy minimization

[farial tavakoli]

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction 
situations? 
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800? 
Thank in advanceFarial

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[gmx-users] charmm36 force field

[farial tavakoli]

Dear GMX users
I used charmm36 force field to run MD simulation on my receptor and ligand 
which has 2 phosphotyrosine groups. All of steps that I did are following as:

1) gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh -his2) gmx editconf -f .gro 
-o newbox.gro -c -d 1.0 -bt dodecahedron3)gmx solvate -cp newbox.gro -cs 
tip4p.gro -p .top -o .gro 4) gmx grompp -f ions.mdp -c .gro -p .top -o 
ions.tpr5) gmx genion -s ions.tpr -o .gro -p .top -pname NA -np 11 -nname CL6) 
gmx frompp -f minim.mdp -c .gro -p .top -o em.tpr7) gmx mdrun -v -deffnm em
ions.mdp and minim.mdp files:; minim.mdp - used as input into grompp to 
generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps        = 5          ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type        = grid        ; Method to determine neighbor list (simple, 
grid)
coulombtype    = PME        ; Treatment of long range electrostatic 
interactions
rcoulomb    = 1.2        ; Short-range electrostatic cut-off
rvdw        = 1.2        ; Short-range Van der Waals cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)
DispCorr = no

then I checked em.gro using vmd, the ligand was in the active site and there 
was no problem.
8) gmx grompp -f nvt.mdp -c em.gro -p .top -o nvt.tpr9) gmx mdrun -deffnm nvt
nvt.mdp file:
title        = CHARMM36 EGFR NVT equilibration 
define        =  -DUSE_OLD_C3
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 20        ; 2 * 5 = 400 ps
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 500        ; save coordinates every 1.0 ps
nstvout        = 500        ; save velocities every 1.0 ps
nstenergy    = 500        ; save energies every 1.0 ps
nstlog        = 500        ; update log file every 1.0 ps
; Bond parameters
continuation    = no        ; first dynamics run
constraint_algorithm    = lincs    ; holonomic constraints 
constraints    = h-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        ; 20 fs, largely irrelevant with Verlet
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw-switch = 1.0
; Electrostatics
coulombtype    = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16    ; grid spacing for FFT
; Temperature coupling is on
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 is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = no        ; 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
but when I checked nvt.gro by VMD ,  viewed  the receptor and ligand went out 
of the box, almost completely and ligand was separated from the protein, 
completely. Is there anyone who can help me and advice me why it was happened?
best Farial
 



 
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Re: [gmx-users] restart nvt run

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you so so much for your reply
Best regardsFarial


Sent from Yahoo Mail for iPhone


On Sunday, February 4, 2018, 5:22 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 2/4/18 8:50 AM, farial tavakoli wrote:
> Dear Justin
>
> Thank you so much for replying
>  I dont know exactly how I should use gmx trjcat command to 
> concatenate 2 .trr files (nvt.trr and traj.part0002.trr)
> I issued this command to merge them:
>
> gmx trjcat -f nvt.trr -o fixed.trr -cat
>
> but faced to this result:
>
> gmx trjcat -f nvt.trr -o fixed.trr -cat
>

This accomplishes nothing; nvt.trr and fixed.trr will be identical. The 
purpose of trjcat is to assemble multiple trajectory files (note in the 
help information, the -f argument specifies that it takes multiple 
files). You want:

gmx trjcat -f nvt.trr traj.part0002.trr -o fixed.trr

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] restart nvt run

[farial tavakoli]

Dear GMX users
I ran nvt simulation on my complex using gromacs2016.4. But faced to this 
error:File input/output error:
Cannot read/write checkpoint; corrupt file, or maybe you are out of disk
space?

so I deleted some files to make free space and then issued this command to 
restart the simulationgmx mdrun -s nvt.tpr -cpi nvt.cpt but faced to this error:
Output file appending has been requested,
but some output files listed in the checkpoint file nvt.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
  nvt.log
  nvt.trr
  nvt.edr

---
Program: gmx mdrun, version 2016.4
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

"Fatal error:
File appending requested, but 3 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If you used -deffnm and the files
listed above as not present are in fact present, try explicitly specifying
them in respective mdrun options. If the files are not available, you can add
the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead."

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 I renamed my files in this way:nvt.log to md.lognvt.edr to ener.edrnvt.trr to 
traj.trrnvt.cpt to state.cptnvt.tpr to topol.tpr
but faced to the "fatal error" again. is there any one can help me? I dont want 
to use -noappend flag.
thanks in advanceFarial

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[gmx-users] how to make index file for a complex which is composed of protein and a phosphotyrosine ligand

[farial tavakoli]

Dear gmx users
I need to calculate the energy binding of my complex, composed protein and a 
phosphotyrosine ligand, using g_mmpba, but when I wanna make an index file by 
this command:gmx make_ndx -f md_0_1.gro -o index.ndxand type :splitch 1 in 
order to separate the protein and phosphotyrosine ligand , face to this 
elements:
Group 0 ( System) has 67577 elements
Group 1 (    Protein) has  5290 elements
Group 2 (  Protein-H) has  2631 elements
Group 3 (    C-alpha) has   328 elements
Group 4 (   Backbone) has   984 elements
Group 5 (  MainChain) has  1310 elements
Group 6 (   MainChain+Cb) has  1619 elements
Group 7 (    MainChain+H) has  1624 elements
Group 8 (  SideChain) has  3666 elements
Group 9 (    SideChain-H) has  1321 elements
Group    10 (    Prot-Masses) has  5290 elements
Group    11 (    non-Protein) has 62287 elements
Group    12 (  Other) has    48 elements
Group    13 (    TP2) has    48 elements
Group    14 ( NA) has    11 elements
Group    15 (  Water) has 62228 elements
Group    16 (    SOL) has 62228 elements
Group    17 (  non-Water) has  5349 elements
Group    18 (    Ion) has    11 elements
Group    19 (    TP2) has    48 elements
Group    20 ( NA) has    11 elements
Group    21 ( Water_and_ions) has 62239 elements
Group    22 ( Protein_chain1) has  5204 elements
Group    23 ( Protein_chain2) has    86 elements

Group 23 is my ligand but without phosphotyrosine groups. Groups 13 & 19 are 
phosphotyrosine groups. I dont know how I can obtain my ligand with its 
ohosphotyrosine groups.is there anyone can help me?
best Farial
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Re: [gmx-users] TP2 problem

[farial tavakoli]

Dear Justin
Thank you for your replying
best Farial
 

On Wednesday, January 3, 2018, 4:36:38 AM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 1/2/18 4:28 PM, farial tavakoli wrote:
> Dear Justin
> Thank you for replying
> I understood what was the wrong and fixed it. But now I have another problem 
> about CHARMM36 mdp file. I studied 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM for 
> adding new settings to mdp file but I need to understand if It is needed to 
> add these new settings to the mdp file for minimizatin? In fact, I couldnt

The nonbonded settings specified there should be used in all your .mdp 
files when using the CHARMM force field.

> understand what does mean these settings:
> vdw-modifier = force-switchrvdw-switch = 1.0
> Should I add these to the mdp file for minimization?

You should add everything on that page exactly as it appears. If you are 
unclear on what the settings are or mean, read the GROMACS manual and 
CHARMM force field literature.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] TP2 problem

[farial tavakoli]

Dear Justin
Thank you for replying
I understood what was the wrong and fixed it. But now I have another problem 
about CHARMM36 mdp file. I studied 
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM for adding 
new settings to mdp file but I need to understand if It is needed to add these 
new settings to the mdp file for minimizatin? In fact, I couldnt understand 
what does mean these settings:
vdw-modifier = force-switchrvdw-switch = 1.0
Should I add these to the mdp file for minimization?
 

On Tuesday, January 2, 2018, 4:54:09 PM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 1/2/18 8:21 AM, farial tavakoli wrote:
> Dear Justin
> Thank you for replying
> Yes I added TP2 as protein in th residurtype.dat file , but faced to the 
> error agin
>
>  

That's not possible. If you add "TP2 Protein" to residuetypes.dat, 
pdb2gmx will not tell you that TP2 is type "Other." Check your 
modification of residuetypes.dat, and if you don't have permission to 
edit the system-wide accessible file in $GMXLIB, make a copy in the 
working directory and edit that one.

-Justin

>
>      On Tuesday, January 2, 2018, 4:28:38 PM GMT+3:30, Justin Lemkul 
><jalem...@vt.edu> wrote:
>  
>  
>
> On 1/2/18 7:54 AM, farial tavakoli wrote:
>> Dear GMX users
>> I need to generate a topology for my complex (protein + peptide) using 
>> CHARMM36 ff in gromacs , since It has 2 phosphotyrosine residues. I did 
>> these steps:
>> at first , I converted TYR in pdb file to TP2, accordingly the merged.tpr 
>> file of CHARMM36 ff.
>> then , changed P atom in pdb file to P1 and changed O1P,O2P,O3P in pdb file 
>> to O2,O3,O4 , respectively, in accord with merged.tpr file
>>    added TP2 residue to residuetype.dat file as a protein in working 
>>directory
>> My protein has 323 residues , start terminus: GLY 1  and  end terminus : ILE 
>> 323My peptide has 7 residues , start terminus : THR 1  and  end terminus :  
>> PRO 7
>> but when issued this command:
>>    gmx pdb2gmx -f .pdb -o .gro -ignh -water tip4p
>>     faced to this error and warnings:
>> Start terminus GLY-1: GLY-NH3+
>> End terminus ILE-323: COO-
>> Opening force field file ./charmm36-jul2017.ff/merged.arn
>> Checking for duplicate atoms
>> Generating any missing hydrogen atoms and/or adding termini.
>> Now there are 323 residues with 5204 atoms
>> Chain time...
>>
>> Back Off! I just backed up topol_Protein_chain_A.itp to 
>> ./#topol_Protein_chain_A.itp.14#
>> Making bonds...
>> Number of bonds was 5261, now 5261
>> Generating angles, dihedrals and pairs...
>> Before cleaning: 13845 pairs
>> Before cleaning: 14000 dihedrals
>> Keeping all generated dihedrals
>> Making cmap torsions...
>> There are  321 cmap torsion pairs
>> There are 14000 dihedrals,  863 impropers, 9560 angles
>>      13764 pairs, 5261 bonds and 0 virtual sites
>> Total mass 36882.800 a.m.u.
>> Total charge -7.000 e
>> Writing topology
>>
>> Back Off! I just backed up posre_Protein_chain_A.itp to 
>> ./#posre_Protein_chain_A.itp.14#
>> Processing chain 2 'B' (73 atoms, 7 residues)
>> Analysing hydrogen-bonding network for automated assignment of histidine
>>     protonation. 12 donors and 10 acceptors were found.
>> There are 11 hydrogen bonds
>> Will use HISE for residue 2
>> Identified residue THR1 as a starting terminus.
>> Warning: Residue TP23 in chain has different type (Other) from starting 
>> residue THR1 (Protein).
>> Warning: Residue TP24 in chain has different type (Other) from starting 
>> residue THR1 (Protein).
>> Warning: Residue LEU5 in chain has different type (Protein) from starting 
>> residue THR1 (Protein).
>> Warning: Residue LEU6 in chain has different type (Protein) from starting 
>> residue THR1 (Protein).
>> Warning: Residue PRO7 in chain has different type (Protein) from starting 
>> residue THR1 (Protein).
>> Identified residue HIS2 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Start terminus THR-1: NH3+
>> End terminus HIS-2: COO-
>> Opening force field file ./charmm36-jul2017.ff/merged.arn
>>
>> ---
>> Program: gmx pdb2gmx, version 2016.4
>> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
>>
>> Fatal error:
>> Atom OXT in residue PRO 7 was not found in rtp entry PRO with 14 atoms
>> while sorting atoms.
>> .
>>
>> For more information and tips for troubleshooting, please check the 
>> GROMACSwebsite a

Re: [gmx-users] TP2 problem

[farial tavakoli]

yes . I did the same exactly. I made a copy of residutyps.dat file in my 
working directory, edited it and issued pdb2gmx command. but got the same error.
Warning: Residue TP23 in chain has different type (Other) from starting residue 
THR1 (Protein).
Warning: Residue TP24 in chain has different type (Other) from starting residue 
THR1 (Protein).
Warning: Residue LEU5 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Warning: Residue LEU6 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Warning: Residue PRO7 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Identified residue HIS2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus THR-1: NH3+
End terminus HIS-2: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn

---
Program: gmx pdb2gmx, version 2016.4
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)

Fatal error:
Atom OXT in residue PRO 7 was not found in rtp entry PRO with 14 atoms
while sorting atoms.
.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


 

On Tuesday, January 2, 2018, 4:54:09 PM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 1/2/18 8:21 AM, farial tavakoli wrote:
> Dear Justin
> Thank you for replying
> Yes I added TP2 as protein in th residurtype.dat file , but faced to the 
> error agin
>
>  

That's not possible. If you add "TP2 Protein" to residuetypes.dat, 
pdb2gmx will not tell you that TP2 is type "Other." Check your 
modification of residuetypes.dat, and if you don't have permission to 
edit the system-wide accessible file in $GMXLIB, make a copy in the 
working directory and edit that one.

-Justin

>
>      On Tuesday, January 2, 2018, 4:28:38 PM GMT+3:30, Justin Lemkul 
><jalem...@vt.edu> wrote:
>  
>  
>
> On 1/2/18 7:54 AM, farial tavakoli wrote:
>> Dear GMX users
>> I need to generate a topology for my complex (protein + peptide) using 
>> CHARMM36 ff in gromacs , since It has 2 phosphotyrosine residues. I did 
>> these steps:
>> at first , I converted TYR in pdb file to TP2, accordingly the merged.tpr 
>> file of CHARMM36 ff.
>> then , changed P atom in pdb file to P1 and changed O1P,O2P,O3P in pdb file 
>> to O2,O3,O4 , respectively, in accord with merged.tpr file
>>    added TP2 residue to residuetype.dat file as a protein in working 
>>directory
>> My protein has 323 residues , start terminus: GLY 1  and  end terminus : ILE 
>> 323My peptide has 7 residues , start terminus : THR 1  and  end terminus :  
>> PRO 7
>> but when issued this command:
>>    gmx pdb2gmx -f .pdb -o .gro -ignh -water tip4p
>>     faced to this error and warnings:
>> Start terminus GLY-1: GLY-NH3+
>> End terminus ILE-323: COO-
>> Opening force field file ./charmm36-jul2017.ff/merged.arn
>> Checking for duplicate atoms
>> Generating any missing hydrogen atoms and/or adding termini.
>> Now there are 323 residues with 5204 atoms
>> Chain time...
>>
>> Back Off! I just backed up topol_Protein_chain_A.itp to 
>> ./#topol_Protein_chain_A.itp.14#
>> Making bonds...
>> Number of bonds was 5261, now 5261
>> Generating angles, dihedrals and pairs...
>> Before cleaning: 13845 pairs
>> Before cleaning: 14000 dihedrals
>> Keeping all generated dihedrals
>> Making cmap torsions...
>> There are  321 cmap torsion pairs
>> There are 14000 dihedrals,  863 impropers, 9560 angles
>>      13764 pairs, 5261 bonds and 0 virtual sites
>> Total mass 36882.800 a.m.u.
>> Total charge -7.000 e
>> Writing topology
>>
>> Back Off! I just backed up posre_Protein_chain_A.itp to 
>> ./#posre_Protein_chain_A.itp.14#
>> Processing chain 2 'B' (73 atoms, 7 residues)
>> Analysing hydrogen-bonding network for automated assignment of histidine
>>     protonation. 12 donors and 10 acceptors were found.
>> There are 11 hydrogen bonds
>> Will use HISE for residue 2
>> Identified residue THR1 as a starting terminus.
>> Warning: Residue TP23 in chain has different type (Other) from starting 
>> residue THR1 (Protein).
>> Warning: Residue TP24 in chain has different type (Other) from starting 
>> residue THR1 (Protein).
>> Warning: Residue LEU5 in chain has different type (Protein) from starting 
>> residue THR1 (Protein).
>> Warning: Residue LEU6 in chain has different type (Protein) from starting 
>> residue THR1 (Protein).
>> Warning: Residue PRO7 in chain has different type (Protein) from starting 
>> r

Re: [gmx-users] TP2 problem

[farial tavakoli]

Dear Justin
Thank you for replying
Yes I added TP2 as protein in th residurtype.dat file , but faced to the error 
agin

 

On Tuesday, January 2, 2018, 4:28:38 PM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 1/2/18 7:54 AM, farial tavakoli wrote:
> Dear GMX users
> I need to generate a topology for my complex (protein + peptide) using 
> CHARMM36 ff in gromacs , since It has 2 phosphotyrosine residues. I did these 
> steps:
> at first , I converted TYR in pdb file to TP2, accordingly the merged.tpr 
> file of CHARMM36 ff.
> then , changed P atom in pdb file to P1 and changed O1P,O2P,O3P in pdb file 
> to O2,O3,O4 , respectively, in accord with merged.tpr file
>  added TP2 residue to residuetype.dat file as a protein in working directory
> My protein has 323 residues , start terminus: GLY 1  and  end terminus : ILE 
> 323My peptide has 7 residues , start terminus : THR 1  and  end terminus :  
> PRO 7
> but when issued this command:
>  gmx pdb2gmx -f .pdb -o .gro -ignh -water tip4p
>   faced to this error and warnings:
> Start terminus GLY-1: GLY-NH3+
> End terminus ILE-323: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
> Checking for duplicate atoms
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 323 residues with 5204 atoms
> Chain time...
>
> Back Off! I just backed up topol_Protein_chain_A.itp to 
> ./#topol_Protein_chain_A.itp.14#
> Making bonds...
> Number of bonds was 5261, now 5261
> Generating angles, dihedrals and pairs...
> Before cleaning: 13845 pairs
> Before cleaning: 14000 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are  321 cmap torsion pairs
> There are 14000 dihedrals,  863 impropers, 9560 angles
>    13764 pairs, 5261 bonds and 0 virtual sites
> Total mass 36882.800 a.m.u.
> Total charge -7.000 e
> Writing topology
>
> Back Off! I just backed up posre_Protein_chain_A.itp to 
> ./#posre_Protein_chain_A.itp.14#
> Processing chain 2 'B' (73 atoms, 7 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
>   protonation. 12 donors and 10 acceptors were found.
> There are 11 hydrogen bonds
> Will use HISE for residue 2
> Identified residue THR1 as a starting terminus.
> Warning: Residue TP23 in chain has different type (Other) from starting 
> residue THR1 (Protein).
> Warning: Residue TP24 in chain has different type (Other) from starting 
> residue THR1 (Protein).
> Warning: Residue LEU5 in chain has different type (Protein) from starting 
> residue THR1 (Protein).
> Warning: Residue LEU6 in chain has different type (Protein) from starting 
> residue THR1 (Protein).
> Warning: Residue PRO7 in chain has different type (Protein) from starting 
> residue THR1 (Protein).
> Identified residue HIS2 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus THR-1: NH3+
> End terminus HIS-2: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
>
> ---
> Program: gmx pdb2gmx, version 2016.4
> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
>
> Fatal error:
> Atom OXT in residue PRO 7 was not found in rtp entry PRO with 14 atoms
> while sorting atoms.
> .
>
> For more information and tips for troubleshooting, please check the 
> GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> I am confused and dont understand where the problem is? It has taken my time 
> for 2 days. I would really appreciate it if anybody helps me to solve this 
> problem.
> best regardsFarial
>
>

Three people have asked identical questions within the last day. Please 
pay attention to other posts that are on similar topics so we can avoid 
repeating ourselves.

The issue is that you do not have TP2 in residuetypes.dat and properly 
identified as Protein (note the messages above about chain 
discontinuities). Add this and pdb2gmx will work.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] TP2 problem

[farial tavakoli]

Dear GMX users
I need to generate a topology for my complex (protein + peptide) using CHARMM36 
ff in gromacs , since It has 2 phosphotyrosine residues. I did these steps:
at first , I converted TYR in pdb file to TP2, accordingly the merged.tpr file 
of CHARMM36 ff.
then , changed P atom in pdb file to P1 and changed O1P,O2P,O3P in pdb file to 
O2,O3,O4 , respectively, in accord with merged.tpr file
 added TP2 residue to residuetype.dat file as a protein in working directory
My protein has 323 residues , start terminus: GLY 1  and  end terminus : ILE 
323My peptide has 7 residues , start terminus : THR 1  and  end terminus :  PRO 
7
but when issued this command:
 gmx pdb2gmx -f .pdb -o .gro -ignh -water tip4p 
 faced to this error and warnings:
Start terminus GLY-1: GLY-NH3+
End terminus ILE-323: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 323 residues with 5204 atoms
Chain time...

Back Off! I just backed up topol_Protein_chain_A.itp to 
./#topol_Protein_chain_A.itp.14#
Making bonds...
Number of bonds was 5261, now 5261
Generating angles, dihedrals and pairs...
Before cleaning: 13845 pairs
Before cleaning: 14000 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are  321 cmap torsion pairs
There are 14000 dihedrals,  863 impropers, 9560 angles
  13764 pairs, 5261 bonds and 0 virtual sites
Total mass 36882.800 a.m.u.
Total charge -7.000 e
Writing topology

Back Off! I just backed up posre_Protein_chain_A.itp to 
./#posre_Protein_chain_A.itp.14#
Processing chain 2 'B' (73 atoms, 7 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 12 donors and 10 acceptors were found.
There are 11 hydrogen bonds
Will use HISE for residue 2
Identified residue THR1 as a starting terminus.
Warning: Residue TP23 in chain has different type (Other) from starting residue 
THR1 (Protein).
Warning: Residue TP24 in chain has different type (Other) from starting residue 
THR1 (Protein).
Warning: Residue LEU5 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Warning: Residue LEU6 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Warning: Residue PRO7 in chain has different type (Protein) from starting 
residue THR1 (Protein).
Identified residue HIS2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus THR-1: NH3+
End terminus HIS-2: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn

---
Program: gmx pdb2gmx, version 2016.4
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)

Fatal error:
Atom OXT in residue PRO 7 was not found in rtp entry PRO with 14 atoms
while sorting atoms.
.

For more information and tips for troubleshooting, please check the 
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
I am confused and dont understand where the problem is? It has taken my time 
for 2 days. I would really appreciate it if anybody helps me to solve this 
problem. 
best regardsFarial


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[gmx-users] phosphotyrosine

[farial tavakoli]

Dear gmx users
I used CHARMM36 ff to generate topology for my complex which has 2 
phosphotyrosines. when I issed gmx pdb2gmx command , I faced to this error:
Fatal error:
Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
I couldnt understand what it meant . my protein residue 1 is Gly and peptide 
residue 1 is Thr. there is no residue Pro in position 1 in both molecules. In 
addition, I checked merged.rtp file of CHARMM36 ff to compare pro residue in it 
with the input file , but everything sound be ok.  I dont know , what should I 
do. I would really appreciate it if anybody helps me
best Farial
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[gmx-users] to generate phosphotyrosine topology

[farial tavakoli]

Dear gromacs users
I need to generate topology for my protein-peptide complex which the peptide 
has 2 phosphotyrosine residues. I used CHARMM36 force field to do that. I n 
that way, I downloaded this force field from 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and paste it in working 
directory. Then issued :gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh  
selected charmm36 all-atom force fieldfrom the working directorybut at last 
faced to this error:
Fatal error:
Atom P1 in residue TYR 3 was not found in rtp entry TYR with 21 atoms
while sorting atoms.

Is there anyone can help me?
best Farial
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[gmx-users] G-mmpbsa

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I used g_mmpbsa to calculate the binding energy of my complex. But the results 
was positive .Is there anyone can help me how come the calculated total binding 
energy was positive? I searched google, and found it might be because of the 
polar dielectric constant. I increased pdie from 2 as default value to 4. But 
got the same results. ( total energy was pisitive) . I know g_mmpbsa doesnt 
relate to here but  I would really be appreciated it if someone can help me
Thanks in advanceFarial


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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  No I meant my newtrj.xtc file In fact I watched my trajectory 
file before and it was ok


Sent from Yahoo Mail for iPhone


On Friday, November 10, 2017, 7:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 11/10/17 11:22 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Then I ignore that  i cant visualize the protein motion in vmd 
>and go on the left steps of the results quality assuranc?

Watching the trajectory is the most important part of the simulation. 
You need to have matching coordinate and trajectory files.

-Justin

>
> Sent from Yahoo Mail for iPhone
>
>
> On Friday, November 10, 2017, 7:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
> On 11/10/17 11:02 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , 
>>my protein doesnt move at all? I think , it is because of the .gro file has 
>>protein, ligand and sol cordinates , but the newtrj.xtc has just my protein 
>>and ligand. Am i right?
>>    
> Your trajectory and coordinates have to match if you want to visualize.
> If there's a mismatch, VMD prints a clear error that should tell you of
> that fact.
>
> -Justin
>
>>        On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul 
>><jalem...@vt.edu> wrote:
>>    
>>    
>>
>> On 11/10/17 10:35 AM, farial tavakoli wrote:
>>> Dear Justin
>>>
>>> Thank you for replying
>>>
>>> This is my input xtc file :
>>>
>>> gmx check -f md_0_1.xtc
>>>
>>> Checking file md_0_1.xtc
>>> Reading frame   0 time    0.000
>>> # Atoms  49582
>>> Precision 0.001 (nm)
>>> Last frame   1000 time 1.000
>>>
>>>
>>> Item    #frames Timestep (ps)
>>> Step  1001    10
>>> Time  1001    10
>>> Lambda   0
>>> Coords    1001    10
>>> Velocities   0
>>> Forces   0
>>> Box   1001    10
>>>
>>> and this is my output xtc file:
>>>
>>> gmx check -f newtrj.xtc
>>>
>>> Checking file newtrj.xtc
>>> Reading frame   0 time    0.000
>>> # Atoms  3378
>>> Precision 0.001 (nm)
>>> Last frame   1000 time 1.000
>>>
>>>
>>> Item    #frames Timestep (ps)
>>> Step  1001    10
>>> Time  1001    10
>>> Lambda   0
>>> Coords    1001    10
>>> Velocities   0
>>> Forces   0
>>> Box   1001    10
>>>
>> These outputs do not support your assertion that newtrj.xtc only
>> contains one frame. Clearly both the old and new trajectories have the
>> full 1001 frames.
>>
>> -Justin
>>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Then I ignore that  i cant visualize the protein motion in vmd 
and go on the left steps of the results quality assuranc?


Sent from Yahoo Mail for iPhone


On Friday, November 10, 2017, 7:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 11/10/17 11:02 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , 
>my protein doesnt move at all? I think , it is because of the .gro file has 
>protein, ligand and sol cordinates , but the newtrj.xtc has just my protein 
>and ligand. Am i right?
>  

Your trajectory and coordinates have to match if you want to visualize. 
If there's a mismatch, VMD prints a clear error that should tell you of 
that fact.

-Justin

>
>      On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul 
><jalem...@vt.edu> wrote:
>  
>  
>
> On 11/10/17 10:35 AM, farial tavakoli wrote:
>> Dear Justin
>>
>> Thank you for replying
>>
>> This is my input xtc file :
>>
>> gmx check -f md_0_1.xtc
>>
>> Checking file md_0_1.xtc
>> Reading frame   0 time    0.000
>> # Atoms  49582
>> Precision 0.001 (nm)
>> Last frame   1000 time 1.000
>>
>>
>> Item    #frames Timestep (ps)
>> Step  1001    10
>> Time  1001    10
>> Lambda   0
>> Coords    1001    10
>> Velocities   0
>> Forces   0
>> Box   1001    10
>>
>> and this is my output xtc file:
>>
>> gmx check -f newtrj.xtc
>>
>> Checking file newtrj.xtc
>> Reading frame   0 time    0.000
>> # Atoms  3378
>> Precision 0.001 (nm)
>> Last frame   1000 time 1.000
>>
>>
>> Item    #frames Timestep (ps)
>> Step  1001    10
>> Time  1001    10
>> Lambda   0
>> Coords    1001    10
>> Velocities   0
>> Forces   0
>> Box   1001    10
>>
> These outputs do not support your assertion that newtrj.xtc only
> contains one frame. Clearly both the old and new trajectories have the
> full 1001 frames.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , 
my protein doesnt move at all? I think , it is because of the .gro file has 
protein, ligand and sol cordinates , but the newtrj.xtc has just my protein and 
ligand. Am i right? 
 

On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul 
<jalem...@vt.edu> wrote:  
 
 

On 11/10/17 10:35 AM, farial tavakoli wrote:
> Dear Justin
>
> Thank you for replying
>
> This is my input xtc file :
>
> gmx check -f md_0_1.xtc
>
> Checking file md_0_1.xtc
> Reading frame   0 time    0.000
> # Atoms  49582
> Precision 0.001 (nm)
> Last frame   1000 time 1.000
>
>
> Item    #frames Timestep (ps)
> Step  1001    10
> Time  1001    10
> Lambda   0
> Coords    1001    10
> Velocities   0
> Forces   0
> Box   1001    10
>
> and this is my output xtc file:
>
> gmx check -f newtrj.xtc
>
> Checking file newtrj.xtc
> Reading frame   0 time    0.000
> # Atoms  3378
> Precision 0.001 (nm)
> Last frame   1000 time 1.000
>
>
> Item    #frames Timestep (ps)
> Step  1001    10
> Time  1001    10
> Lambda   0
> Coords    1001    10
> Velocities   0
> Forces   0
> Box   1001    10
>

These outputs do not support your assertion that newtrj.xtc only 
contains one frame. Clearly both the old and new trajectories have the 
full 1001 frames.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
I am tryinig to analyz minimum distance between periodic images, so need a new 
.xtc file which has not jumps. I isseued this command:Gmx trjconv -s .tpr -f 
.xtc -o new.xtc -center -pbc molI didnt need to create an index file, because 
my protein and peptide ligand are merged. But when I bring the .gro  and 
new.xtc files  to vmd, the new.xtc file has just a frameWould you please help 
me how come this xtc file has just a frame and what kind of command I have to 
issue to generate a new one? 
Thanks in advanceFarial


Sent from Yahoo Mail for iPhone


On Saturday, October 7, 2017, 8:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/5/17 3:52 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> I performed NVT equilibration for 300 ps , it was done successfully. 
> Yesterday I wanna do NPT equilibration , so used your npt.mdp file in the 
> GROMACS tutorial and replaced energgroups and tc-groups by Protein and 
> Protein water-ions, respectively, specified nstep = 15 , but when I 
> entered, noticed I had md.log file not npt.log. and it runs to 272000 steps . 
> Why?Would you please help me how come it runs this way?

In the absence of your exact sequence of commands, there's nothing to 
say other than you've probably lost track of what you (think you) are doing.

-Justin

>
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@gromacs.org
>  Sent: Wednesday, 4 October 2017, 15:19:38
>  Subject: Re: [gmx-users] peptide ligand
>    
>
>
> On 10/3/17 1:51 PM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Because in tuturial , energygroups = protein JZ4So I think ,I 
>>have to seperate my ligand and Protein in .mdp files and determine H bonds?
>>
> It has nothing to do with the .mdp file. If you want to analyze hydrogen 
> bonds,
> then you can create an .ndx file later for use with gmx hbond.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


 

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[gmx-users] Gmx minimdist

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I am trying to analyz the minimum distance between periodic images,l and need 
to use  the .xtc file without jump, so issued gmx trjconv:Gmx trjconv -f .xtc  
-o new file.xtc -pbc nojump -center
But when bring my .gro and new .xtc files in vmd , my new xtc file has still 
jumps. I studied gmx trjconv maneytimes but couldnt issue a command that works 
well. Would you please clear gmx trjconv to me?I would be really appreciated it 
if someone clarify it to me. 
Thanks in advanceFarial
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[gmx-users] Trjconv

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }   Dear gromacs users
I minimized my complex ( protein-peptide) by:
Gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tprGmx mdrun -v 
-deffnm em
Now I need to view the em.gro file to check if my ligand is placed in the 
pocket? So I created this command and I wanted to know if it is correct?
Gmx trjconv -s em.tpr -f em.gro -o em.pdb -pbc nojump
Thanks in advanceFarial




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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Because in tuturial , energygroups = protein JZ4So I think ,I 
have to seperate my ligand and Protein in .mdp files and determine H bonds? 


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 8:56 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/3/17 1:08 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  So how should I split protein and ligand from each other to 
>create  .mdp files?
> 

I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index 
files 
and now .mdp files? I'm lost, and it's very hard to provide help.

If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part 
of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/3/17 11:13 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Thanks alot for your advxe
>> I would really appreciate if you advice me more to split protein and ligand 
>> in index file, I saw the index help , but couldnt find out how should I use 
>> “ ‘splitch’ nr “ script to split them.
>> With best regardsFarial
>>
> 
> Index files aren't used with pdb2gmx. The splitting functions of make_ndx 
> break
> a chain down into its component residues. That's not at all what you want to 
> do.
> 
> -Justin
> 
>>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>
>> On 10/3/17 9:17 AM, ‪farial tavakoli‬ ‪ wrote:
>>> Dear Justin
>>>
>>> Thank you so much for your reply.
>>> You mean , I should generate a topology file for my complex instead of
>>> creating topology for each of them separately ?
>>>
>>
>> As long as the protein and peptide ligand are denoted as being in
>> separate chains (different chain ID or use of TER in the PDB file), then
>> pdb2gmx will do everything for you.
>>
>> -Justin
>>
>>>
>>>
>>> 
>>> *From:* Justin Lemkul <jalem...@vt.edu>
>>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>>> <farial.tavak...@ymail.com>
>>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>>> *Subject:* Re: [gmx-users] peptide ligand
>>>
>>>
>>>
>>> On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
>>>> Dear GROMACS users
>>>> I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>>> was Protein_chain_B) and converted it to .itp file to string it in
>>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>>> directive to create one topology file for my complex. Created newbox
>>> and solvate.
>>>
>>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>>> multiple
>>> chains natively without any additional effort on your part.
>>>
>>> -Justin
>>>
>>>
>>>> But when I gave this command:gmx grompp -f em_real.mdp -c
>>> solv_ions.gro -p topol.top -o em.tpr
>>>>
>>>> I faced to this error:
>>>>
>>>> Group Protein_chain_B referenced in the .mdb 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.
>>>>
>>>> In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>>> Protein_chain_B , but GROMACS gives error.
>>>> Would you please advice me how can I solve this problem?
>>>>
&

Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Oh I am sorry. Yes  I am trying to run md on my protein peptide 
complex. At first you advice me to use pdb2gmx to generate a topology for my 
complex and  I did. Then  according to the protein ligand complex tuturial in 
gromacs, I defined newbox and solvate After adding ions, I need to do energy 
minimization and use .mdp file which I should specify energygrouos , But my 
protein and ligand are not sepearate from each other. I just eant to know isnt 
there any problem if protein and ligand are merged and not separated?
Best regardsFarial 


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 8:56 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/3/17 1:08 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  So how should I split protein and ligand from each other to 
>create  .mdp files?
> 

I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index 
files 
and now .mdp files? I'm lost, and it's very hard to provide help.

If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part 
of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/3/17 11:13 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Thanks alot for your advxe
>> I would really appreciate if you advice me more to split protein and ligand 
>> in index file, I saw the index help , but couldnt find out how should I use 
>> “ ‘splitch’ nr “ script to split them.
>> With best regardsFarial
>>
> 
> Index files aren't used with pdb2gmx. The splitting functions of make_ndx 
> break
> a chain down into its component residues. That's not at all what you want to 
> do.
> 
> -Justin
> 
>>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>
>> On 10/3/17 9:17 AM, ‪farial tavakoli‬ ‪ wrote:
>>> Dear Justin
>>>
>>> Thank you so much for your reply.
>>> You mean , I should generate a topology file for my complex instead of
>>> creating topology for each of them separately ?
>>>
>>
>> As long as the protein and peptide ligand are denoted as being in
>> separate chains (different chain ID or use of TER in the PDB file), then
>> pdb2gmx will do everything for you.
>>
>> -Justin
>>
>>>
>>>
>>> 
>>> *From:* Justin Lemkul <jalem...@vt.edu>
>>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>>> <farial.tavak...@ymail.com>
>>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>>> *Subject:* Re: [gmx-users] peptide ligand
>>>
>>>
>>>
>>> On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
>>>> Dear GROMACS users
>>>> I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>>> was Protein_chain_B) and converted it to .itp file to string it in
>>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>>> directive to create one topology file for my complex. Created newbox
>>> and solvate.
>>>
>>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>>> multiple
>>> chains natively without any additional effort on your part.
>>>
>>> -Justin
>>>
>>>
>>>> But when I gave this command:gmx grompp -f em_real.mdp -c
>>> solv_ions.gro -p topol.top -o em.tpr
>>>>
>>>> I faced to this error:
>>>>
>>>> Group Protein_chain_B referenced in the .mdb file was not found in
>>> the index file. Group names must match either [moleculety

Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  So how should I split protein and ligand from each other to 
create  .mdp files?


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/3/17 11:13 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Thanks alot for your advxe
> I would really appreciate if you advice me more to split protein and ligand 
> in index file, I saw the index help , but couldnt find out how should I use “ 
> ‘splitch’ nr “ script to split them.
> With best regardsFarial
> 

Index files aren't used with pdb2gmx. The splitting functions of make_ndx break 
a chain down into its component residues. That's not at all what you want to do.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/3/17 9:17 AM, ‪farial tavakoli‬ ‪ wrote:
>> Dear Justin
>>
>> Thank you so much for your reply.
>> You mean , I should generate a topology file for my complex instead of
>> creating topology for each of them separately ?
>>
> 
> As long as the protein and peptide ligand are denoted as being in
> separate chains (different chain ID or use of TER in the PDB file), then
> pdb2gmx will do everything for you.
> 
> -Justin
> 
>>
>>
>> 
>> *From:* Justin Lemkul <jalem...@vt.edu>
>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>> <farial.tavak...@ymail.com>
>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>> *Subject:* Re: [gmx-users] peptide ligand
>>
>>
>>
>> On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
>>> Dear GROMACS users
>>> I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>> was Protein_chain_B) and converted it to .itp file to string it in
>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>> directive to create one topology file for my complex. Created newbox
>> and solvate.
>>
>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>> multiple
>> chains natively without any additional effort on your part.
>>
>> -Justin
>>
>>
>>> But when I gave this command:gmx grompp -f em_real.mdp -c
>> solv_ions.gro -p topol.top -o em.tpr
>>>
>>> I faced to this error:
>>>
>>> Group Protein_chain_B referenced in the .mdb 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.
>>>
>>> In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>> Protein_chain_B , but GROMACS gives error.
>>> Would you please advice me how can I solve this problem?
>>>
>>> Best
>>> Farial
>>
>>>
>>>
>>
>> -- 
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu <mailto:jalem...@vt.edu> | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>>
>> ==
>>
>>
> 

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Thanks alot for your advxe
I would really appreciate if you advice me more to split protein and ligand in 
index file, I saw the index help , but couldnt find out how should I use “ 
‘splitch’ nr “ script to split them. 
With best regardsFarial


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  wrote:



On 10/3/17 9:17 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
>
> Thank you so much for your reply.
> You mean , I should generate a topology file for my complex instead of 
> creating topology for each of them separately ?
>

As long as the protein and peptide ligand are denoted as being in 
separate chains (different chain ID or use of TER in the PDB file), then 
pdb2gmx will do everything for you.

-Justin

>
>
> 
> *From:* Justin Lemkul 
> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪ 
> 
> *Sent:* Tuesday, 3 October 2017, 16:35:49
> *Subject:* Re: [gmx-users] peptide ligand
>
>
>
> On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
> > Dear GROMACS users
> > I need to run a MD on my Protein-peptide ligand complex in GROMACS. 
> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes] 
> was Protein_chain_B) and converted it to .itp file to string it in 
> Protein.top file, then, added Protein_chain_B in [ molecules ] 
> directive to create one topology file for my complex. Created newbox 
> and solvate.
>
> You shouldn't have to do any topology manipulation. pdb2gmx handles 
> multiple
> chains natively without any additional effort on your part.
>
> -Justin
>
>
> > But when I gave this command:gmx grompp -f em_real.mdp -c 
> solv_ions.gro -p topol.top -o em.tpr
> >
> > I faced to this error:
> >
> > Group Protein_chain_B referenced in the .mdb 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.
> >
> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is 
> Protein_chain_B , but GROMACS gives error.
> > Would you please advice me how can I solve this problem?
> >
> > Best
> > Farial
>
> >
> >
>
> -- 
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu  | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
>
> ==
>
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thanks alot for your advice 


Sent from Yahoo Mail for iPhone


On Thursday, August 24, 2017, 5:51 AM, Justin Lemkul <jalem...@vt.edu> wrote:



On 8/21/17 5:25 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; } Hi justin
> Thank you so much for replyingAccording to the gromacs tuturial, i am trying 
> to analyse my complex in terms of RMSD. In order to do that, first it is 
> needed to obtain the average structure to get RMSD vs average structure . And 
> average structure is a side product of obtaining RMSF. Is there anyway that i 
> can calculate RMSD instead of geting RMSD vs average structure? If you want 
> to caculate RMSD , wont you perform this way?

I normally compute RMSD vs. the equilibrated structure or vs. the 
crystal structure, not an average structure.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Hi justin
Thank you so much for replyingAccording to the gromacs tuturial, i am trying to 
analyse my complex in terms of RMSD. In order to do that, first it is needed to 
obtain the average structure to get RMSD vs average structure . And average 
structure is a side product of obtaining RMSF. Is there anyway that i can 
calculate RMSD instead of geting RMSD vs average structure? If you want to 
caculate RMSD , wont you perform this way? 
Thanks in advanceFarial

Sent from Yahoo Mail for iPhone


On Monday, August 21, 2017, 5:24 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 8/20/17 11:48 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear justin
> Thank you for your replyIt means, there is no problem, i can ignore it ang go 
> ahead?

Sure, but keep in mind that this "average structure" has no physical 
meaning.  The B-factors are (possibly) useful, but also keep in mind 
that solution dynamics and crystal dynamics are very different, so 
comparing the two may or may not be useful.

-Justin
> Sent from Yahoo Mail for iPhone
>
>
> On Monday, August 21, 2017, 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
> On 8/20/17 11:51 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Dear gmx users
>> I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
>> complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
>> same .xtc file which was created after using gmx trjconv, but when i view 
>> average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
>> Would you please advice me how to solve this problem?
> There is no physical significance to an average set of coordinates.  These may
> appear broken or distorted.
>
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyIt means, there is no problem, i can ignore it ang go 
ahead? 

Sent from Yahoo Mail for iPhone


On Monday, August 21, 2017, 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:



On 8/20/17 11:51 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gmx users
> I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
> complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
> same .xtc file which was created after using gmx trjconv, but when i view 
> average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
> Would you please advice me how to solve this problem?

There is no physical significance to an average set of coordinates.  These may 
appear broken or distorted.

http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
same .xtc file which was created after using gmx trjconv, but when i view 
average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
Would you please advice me how to solve this problem? 
Best Farial


Sent from Yahoo Mail for iPhone
 
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[gmx-users] Pbc

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs users
I need to visualize my md_0_1.tpr , so i issued  trjconv -s md_0_1.tpr -f 
md_0_1.xtc -o xxx.pdb -pbc nojump -dt 10to remove the jumps over the boundaries 
and make a continuous trajectoryPBCBut when i visualized my complex by pymol, 
the protein appeared broken . Would you please help me to solve it?
BestFarial


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Re: [gmx-users] ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }   Dear justin
Thank you so much 
Yours sincerelyFarial


Sent from Yahoo Mail for iPhone


On Monday, August 14, 2017, 4:35 PM, Justin Lemkul  wrote:



On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to create a .gro file from the united 
> atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
> xxx.gro
> but faced to this warning:
> WARNING: all CONECT records are ignored
> would you please advice me how can i solve this problem?

You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyI thought that topology file obtained from ATB needs to 
be changed like PRODRG


Sent from Yahoo Mail for iPhone


On Sunday, August 13, 2017, 8:43 PM, Justin Lemkul  wrote:



On 8/13/17 3:13 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear GROMACS users
> 
> I noticed my ligand has some broken bonds and changes in atoms arrengement 
> after md simulation was done. I have read before that no bond is broken and 
> created in simulation . So why have been ligand changed ?
> I think, i have to notice that when i wanted to create a ligand topology , i 
> used ATB server to create topology and pdb files. and when wanted to reassign 
> the charges and charge groups, noticed that some of the atoms of ligand that 
> have to be in a charge group, were not successive  , so decided to rearrange 
> them and replaced them to place them in a charge group.

Why did you modify the topology?  Usually ATB topologies require no 
modification.  If you "rearranged" atoms in any way, then you irreparably broke 
the topology because no all of the bonded interactions are nonsense.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] remove the jumps over the boundaries

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Thank you s much


Sent from Yahoo Mail for iPhone


On Wednesday, August 9, 2017, 5:36 PM, Milan Melichercik 
 wrote:

‎Hi,
The message says you have used older Gromacs for analysis than was the tpr file 
was created with. For 2016.x versions you have to use "gmx trjconv" instead of 
plain trjconv. The trjconv you have called is probably from your Linux 
distribution and in old version - you can find its binary file using "which 
trjconv"‎.
BTW why do you store the output to odb file? Cause it will be huge. You should 
extract only one frame (starting/final) using -dump and than the whole 
trajectory to xtc file (sure you can use -dt switch or you can skip frames in 
VMD during the load of xtc file).

Best,

Milan

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: ‪farial tavakoli‬ ‪
Sent: streda, 9. augusta 2017 14:18
To: Discussion List for GROMACS Users
Reply To: gmx-us...@gromacs.org
Subject: [gmx-users] remove the jumps over the boundaries

Dear GROMACS users
I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to 
visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD 
, it has pbc problem, so I issued this command:
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10
but faced to this error:
Fatal error:
reading tpx file (md_0_1.tpr) version 110 with version 83 program

is anybody help me to solve this problem?
thanks in advanceFarial
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Re: [gmx-users] Visualization of xtc file

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi andrea
Thank you for replyYes i moved the speed control on the left but it wasnt 
affected. And now i went to graphical reprezentation and increased trajectory 
smoothing windows size but it was not ok too. It seems my protein has many 
aberrant bonds 

Sent from Yahoo Mail for iPhone


On Monday, August 7, 2017, 2:24 PM, Andrea Spitaleri <andrea.spital...@iit.it> 
wrote:

Hi

please refer to VMD guide/manual/mailing list. You have different 
options to "decrease" the motion:

1. in VMD Main there is a speed control, just move to left with mouse

or/and

2.  in Graphical Representations under Trajectory tab you can increase 
the number of "Trajectory Smoothing Window Size".

HTH

and


On 07/08/2017 11:38, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gromacs user
> I am trying to view .gro and .xtc files of my complex by VMD but when i load 
> first .gro and then .xtc files in vmd , it has so high motion , such that no 
> molecules are viewable. Would you please help me how can i view it?
> ThanksFarial
>
>
> Sent from Yahoo Mail for iPhone
>  

-- 
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557

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[gmx-users] Visualization of xtc file

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am trying to view .gro and .xtc files of my complex by VMD but when i load 
first .gro and then .xtc files in vmd , it has so high motion , such that no 
molecules are viewable. Would you please help me how can i view it?
ThanksFarial


Sent from Yahoo Mail for iPhone
 
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Re: [gmx-users] Gmx hbond

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have 
tc_groups = protein non-protein , it is best to consider protein and ligand as 
one single entity. So we use make-ndx to merg them. When i issue gmx hbond 
there isnt any ligand in this list to choose. How can i determine h bonds 
between protein and ligan , even in my project that is about HDAC2 and my 
designed drug
Thank you Farial



Sent from Yahoo Mail for iPhone


On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul <jalem...@vt.edu> wrote:



On 8/4/17 11:13 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gromacs user
> I am performing protein ligand complex (t4lysosim) and now i need to analyze 
> JZ4 hydrogen bonding, but when i type Gmx hbondThere is no JZ4 in the list to 
> choose. It is because of i used :Gmx make_ndx -f em.gro -o index.ndxAnd 
> merged the " protein " and " JZ4" groupsIs there anyone help me how to check 
> the hydrogen bond of JZ4 ligand?

Both protein and ligand are default groups and do not require the use of an 
index file.  If the ligand isn't showing up in the list, it's probably because 
you're supplying an index file from which the ligand group has been deleted.

-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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[gmx-users] Ligand topology

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs users
Is there any way to create ligand topology file by using pdb2gmx instead of 
prodrg? Because i use gromos 43a1 ff for making protein topology and use prodrg 
to create ligand topoligy and .gro file. But i dont know anything about 
reparametrizing the ligand topology but reassigning charge and charge groups. 
Is there anyone can help me:1) is it possible to make ligand topology file by 
pdb2gmx 2) what kind of reparametrizations are needed to be done to obtain the 
proper ligand topol.top file but reassigning charges and charge groups that 

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Re: [gmx-users] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-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] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-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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[gmx-users] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  HiI am a new GROMACS user and i am trying to run a 
simulation on 4LY1 protein and my designed drug to check their interaction I 
used gromos 43a1 force field and when i performed equilibration with NVT.mdp 
file , I faced this error: step 1: One or more water molecules can not be 
settled. Check for bad contacts and/or reduce the timestep if appropriateI 
really appropriate if anybody can help meThanks alotFarialI typed this command  
gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
gmx mdrun -deffnm nvtThe nvt. Mdp file which i used:
title   = Protein-ligand complex NVT equilibration 
define  = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
energygrps  = Protein DRG
; 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; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.4   ; 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_DRG Water_and_ions; 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

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[gmx-users] Fw: EQUILIBRATION

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi Would you please help me how can i solve my problem ? I wanna 
to do equilibrate my complex ( 4ly1 + ligand) but when use the nvt.mdp file in 
protein -ligand complex (lysosym4) tuturial in gromacs , i faced to an error:   
 step 1: One or more water molecules can not be settled. Check for bad contacts 
and/or reduce the timestep if appropriateThanks alotFarial


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Begin forwarded message:

On Wednesday, July 5, 2017, 6:31 PM, ‪farial tavakoli‬ ‪ 
 wrote:

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but 
when I wanted to performance equilibration , i got this ERROR:  
step 1: One or more water molecules can not be settled. 
 Check for bad contacts and/or reduce the timestep if appropriate
Would you please help me to fix this problem?
These are all stages which I did:
I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands 
and water molecules from it and left just chain A and HETATM ZN A . 
I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx 
-f 4LY1.pdb -o 4LY1.gro -water spc
then made a complex.gro file which include 4LY1.gro and DRG.gro which i got 
from PRODRG site. I also copy paste ; Include ligand topology
#include "DRG.itp"

in the topology file and added DRG as a ligand in [ molecules ] directive. 
Then I defined box by using this command :
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

then defined solvate by :
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

then used grommp to assemble a .tpr file by using a .mdp file and this command :
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

that was my .mdp afile :
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and added 2 CL ions since my total charge was 2.00 because of zn ion. 

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2

then for minimization, i replaced energygroups from system to protein DRG in 
em_real.mdp. that was my em_real.mdp file:

integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol 
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = protein DRG   ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p 
topol.top -o em.tprand
gmx mdrun -v -deffnm em

GROMACS replies:
Steepest Descents converged to Fmax < 1000 in 1833 steps
Potential Energy  = -5.6356275e+05
Maximum force =  9.7815100e+02 on atom 3452
Norm of force =  3.1465845e+01

Simulation ended prematurely, no performance report will be written.
Is there any problem that simulation ended prematurely?

Then