Re: [gmx-users] (no subject)

[Najamuddin Memon]

It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.

On Wed, Dec 25, 2019, 8:54 PM nupur munjal  wrote:

> Hi,
> i am trying to make the index file without loops and termini and using the
> option protein and ligand that is 1 and 13 but the index file is formed
> with the same as it is formed from the whole system.
>
> --
> Kind Regards
> Nupur Munjal
> PhD Scholar (Bioinformatics)
> Department of Biotechnology & Bioinformatics
> Jaypee University of Information Technology
> Waknaghat, Solan,India
>
> The only thing that overcomes hard luck is hard work - Harry Golden
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Re: [gmx-users] segmentation fault core dumped

[Najamuddin Memon]

First of all optimize the geometry of protein by using wincoot especially
considering your respective atom/molecule/amino acid
Change the algorithm of energy minimization to conjugate gradient
If you can see the respective atom it is in collision with any other atom
in any visualization tool. This can be resolved by using wincoot



On Thu, Nov 14, 2019, 4:18 PM Yogesh Sharma  wrote:

> Greetings everyone
>
> I was following protein ligand complex tutorial.
>
> EM run was fine even with double precision.
>
> Steepest Descents converged to Fmax < 1000 in 101 steps
> Potential Energy  = -2.71399964872904e+06
> Maximum force =  9.15885947946535e+02 on atom 4411
> Norm of force =  1.98296351352040e+01
>
> But when I proceeded to nvt or npt equlibriation run. I am getting
>
> starting mdrun 'SOL'
> 5 steps,100.0 ps.
>  segmental fault core dumped.
>
> To troubleshoot I checked .gro file for atom 4411.
>
> 459TRPNE1 4411   5.806   5.696   4.267
>
> 33678SOL OW 4411   5.925  11.717   8.738
>
> I am attaching picture here for 4411 atom containing residues for
> reference.
>
> Both of the atoms are inside box parameters.
>
>  I even decreased temperature to 1K  or  30K but all in vain
>
> Can you help me with this? Thank you.
>
>  *  with  regards*
> *Yogesh Sharma*
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Re: [gmx-users] How to produce "gro" format for calcite {1014} structure.

[Najamuddin Memon]

Please obtain topology of calcite (1014) from prodrg and you can also see
protein-ligand simulation protocol of gromacs exactly follow it.

On Tue, Nov 12, 2019, 9:09 PM Hamid Zaree  wrote:

> Hi.
> I would like to simulate Calcite structure in GROMACS. How could I make the
> structure of Calcite {1014}. And how could I make its topology.
> I was found a cif file in AMCSD data bank and a python script which
> produced a favourable shape of Calcite "gro" file; but:
>
> 1- The downloaded "Cif" file is not 1014 symmetry structure.
> 2- The final "gro" file (after implementing that python) has not molecule
> type and unfortunately, all Oxygen atoms as well the "Ca" and "C" came
> along each other and each Oxygen atom considered as a molecule in this
> "gro" file. In this case, I wasn't able to make a proper topology file. by
> any means.
> Special thanks!
> Shahryar.
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Re: [gmx-users] Error in DNA.itp file

[Najamuddin Memon]

Residue type.dat file having definition of nucleotides

On Tue, Nov 5, 2019, 9:55 PM Najamuddin Memon 
wrote:

> You may use Amber99sb force field  for DNA-protein simulation and also put
> residue type.dat file in your folder. It will work
>
>
> On Tue, Nov 5, 2019, 6:59 PM Paul bauer  wrote:
>
>> Hello,
>>
>> the error states that you are missing parameters for your system. Did
>> you check that the forcefield contains all the special parameters you
>> need for the conjugate molecule?
>> Also, I would recommend to not use a prehistoric version of GROMACS for
>> new studies, if there are no specific reasons preventing you from using
>> a more recent one that is still supported (such as 2018 or 2019).
>>
>> Cheers
>>
>> Paul
>>
>> On 05/11/2019 14:47, Ayesha Kanwal wrote:
>> > Hi all,
>> > i am preparing system of DNA-protein complex, downloaded it from RCSB
>> website, by using GROMACS-version 4.5.5; force field AMBER03WS with water
>> Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type.
>> > but the problem is that when i use command for energy minimization the
>> following error has occurred. Error shows that problem is in .itp file Dih.
>> types. For protein .itp files,there was no problem. Only DNA .itp files
>> have issue. Its my first time i am preparing this kind of system please let
>> me know how can i resolve this problem and why these errors were generated
>> ? I have searched out previous mail but could not find relevant answer so i
>> am posting it now here. i have attached .mdp file with this e-mail.
>> >
>> > checking input for internal consistency...
>> > Generated 2412 of the 2415 non-bonded parameter combinations
>> > Generating 1-4 interactions: fudge = 0.5
>> > Generated 2415 of the 2415 1-4 parameter combinations
>> >
>> > ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]:
>> >No default Improper Dih. types
>> >
>> >
>> > ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]:
>> >No default Improper Dih. types
>> >
>> >
>>
>> --
>> Paul Bauer, PhD
>> GROMACS Release Manager
>> KTH Stockholm, SciLifeLab
>> 0046737308594
>>
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Re: [gmx-users] Error in DNA.itp file

[Najamuddin Memon]

You may use Amber99sb force field  for DNA-protein simulation and also put
residue type.dat file in your folder. It will work


On Tue, Nov 5, 2019, 6:59 PM Paul bauer  wrote:

> Hello,
>
> the error states that you are missing parameters for your system. Did
> you check that the forcefield contains all the special parameters you
> need for the conjugate molecule?
> Also, I would recommend to not use a prehistoric version of GROMACS for
> new studies, if there are no specific reasons preventing you from using
> a more recent one that is still supported (such as 2018 or 2019).
>
> Cheers
>
> Paul
>
> On 05/11/2019 14:47, Ayesha Kanwal wrote:
> > Hi all,
> > i am preparing system of DNA-protein complex, downloaded it from RCSB
> website, by using GROMACS-version 4.5.5; force field AMBER03WS with water
> Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type.
> > but the problem is that when i use command for energy minimization the
> following error has occurred. Error shows that problem is in .itp file Dih.
> types. For protein .itp files,there was no problem. Only DNA .itp files
> have issue. Its my first time i am preparing this kind of system please let
> me know how can i resolve this problem and why these errors were generated
> ? I have searched out previous mail but could not find relevant answer so i
> am posting it now here. i have attached .mdp file with this e-mail.
> >
> > checking input for internal consistency...
> > Generated 2412 of the 2415 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 2415 of the 2415 1-4 parameter combinations
> >
> > ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]:
> >No default Improper Dih. types
> >
> >
> > ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]:
> >No default Improper Dih. types
> >
> >
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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Re: [gmx-users] Pro-Lig Error

[Najamuddin Memon]

Remove coordinates of ligand from .pdb file as you call coordinates of
ligands two times first from .pdb file and second by putting drg.itp
calling from .top file


On Sun, Oct 6, 2019, 9:30 PM Iman Katouzian  wrote:

> Hello,
>
> I have simulated a protein-ligand file and produced the ligand file by
> antechamber software using the Amber03 force field. All the stages in
> Gromacs were performed correctly without any error however when I ran this
> code :
>
> gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr
> I encounter this error:
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 40906)
>  does not match topology (topol.top, 40950)
>
> I just performed my simulation many times but I could not pass this error.
>
> Thanks
>
>
>
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
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Re: [gmx-users] Protein ligand simulation

[Najamuddin Memon]

you should follow steps from protein-Ligand simulation. Write in google "
www.bevanlab.biochem.vt.edu › justin › gmx-tutorials › complex_old
".
Take coordinates of JZ4 from PRODRG.


   1.
   




On Tue, Oct 1, 2019 at 12:39 PM DEEPANSHU SINGLA <
deepanshusingl...@gmail.com> wrote:

> I am trying to learn protein ligand simulation. I tried to follow the steps
> for lysozyme using the GROMACS tutorial. I received the following error:
>
> *ERROR 1 {file jz4.itp, line 183]:*
> * No default Proper Dih. types*
>
>
> *ERROR 2 [file jz4.itp, line 194]:*
> * No default Proper Dih. types*
>
> *Fatal error: *
> *Syntax error -File forcefield.itp, line 10*
> *Last line resd:*
> *'[defaults]'*
> *Invalid order for directive defaults*
>
> Please help me resolve this error.
>
> Thanking you in advance.
>
> Deepanshu Singla
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Re: [gmx-users] Protein ligand simulation

[Najamuddin Memon]

First of all take coordinates of ligand  from online available resources
mentioned in protocol of protein ligand simulation and exactly follow the
same you will get simulation run

Regards
Najam

On Sat, Sep 28, 2019, 2:38 PM DEEPANSHU SINGLA 
wrote:

> I am trying to learn protein ligand simulation. I tried to follow the steps
> for lysozyme using the GROMACS tutorial. I received the following error:
>
> *ERROR 1 {file jz4.itp, line 183]:*
> * No default Proper Dih. types*
>
>
> *ERROR 2 [file jz4.itp, line 194]:*
> * No default Proper Dih. types*
>
> *Fatal error: *
> *Syntax error -File forcefield.itp, line 10*
> *Last line resd:*
> *'{defaults]'*
> *Invalid order for directive defaults*
>
> Please help me resolve this error.
>
> Thanking you in advance.
>
> Deepanshu Singla
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Re: [gmx-users] Regarding obtaining potential energy using energy groups

[Najamuddin Memon]

It depends on interaction of proteins i.e A interacts with B
A both interact with C
Only A or only B interacts with C
In 2nd option you can make one group (A) and 2nd group as C

On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 <
nashit.ja...@iitgn.ac.in> wrote:

> I think so that the question is to confirm whether finding potential energy
> making (AB) and C as 2 groups similar to the potential energy obtained by
> adding energies obtained by making A -C and B -C as groups
>
> -Nashit
>
> On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
> najamuddinmemo...@gmail.com> wrote:
>
> > No you should take two groups at a time
> > Like A VS B then A vs C and so on before doing energy analysis you should
> > make index file that you have to call in command line with -n index.ndx
> > Regards
> > Najam
> >
> > On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
> nirali.d.ims...@ahduni.edu.in>
> > wrote:
> >
> > > Dear all
> > > I have a system with 3 protein chains A B and C. I want to calculate
> the
> > > potential energy between different chains.
> > > I created energy groups by creating a new index file.
> > > If I calculate potential energy between  C as one group and (AB) as
> > another
> > > group, will it contain the potential energy of interaction between A
> and
> > B
> > > too?
> > >
> > > Your kind guidance in this matter is highly appreciated.
> > >
> > >
> > > Thanking you,
> > > Nirali Desai
> > > --
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Re: [gmx-users] Regarding obtaining potential energy using energy groups

[Najamuddin Memon]

No you should take two groups at a time
Like A VS B then A vs C and so on before doing energy analysis you should
make index file that you have to call in command line with -n index.ndx
Regards
Najam

On Fri, Sep 13, 2019, 3:21 PM Nirali Desai 
wrote:

> Dear all
> I have a system with 3 protein chains A B and C. I want to calculate the
> potential energy between different chains.
> I created energy groups by creating a new index file.
> If I calculate potential energy between  C as one group and (AB) as another
> group, will it contain the potential energy of interaction between A and B
> too?
>
> Your kind guidance in this matter is highly appreciated.
>
>
> Thanking you,
> Nirali Desai
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Re: [gmx-users] Tyrosine to phosphotyrosine conversion a must in phosphorylation protein ?

[Najamuddin Memon]

Dear Seke

Yes it Is obligatory to phosphorylate the tyrosine. Use 43a1p extended
phosphorylated force field you will get good results after comparing both
non phosphorylated and phosphorylated structures

Regards
Najam



On Wed, Sep 4, 2019 at 7:31 AM Seketoulie Keretsu 
wrote:

> Dear expert,
>
> This is not a gromacs problem however I'm wondering if you can give some
> insight and direction to go look further.
>
> I have a protein phosphorylation protein kinase with a phosphotyrosine at a
> position 20 angstrom away from the binding site. I want to perform an MD to
> study the protein ligand interaction and binding energy calculations. I
> wonder if the modeling of the tyrosine to phophotyrosine is imperative for
> such studies. Is there any review or study done comparing such changes? I
> know newer force fields supports phosphorylation residues but wanted to
> know if failing to use phosphorylation structure would make the study
> useless.
>
> Your inputs will be appreciated.
>
> Thank you.
>
> Sincerely,
>
> Seke
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Re: [gmx-users] Segmentation fault, core dumped error

[Najamuddin Memon]

You can go to gmx hbond tutorial in gromacs.


On Thu, May 30, 2019, 5:12 AM Najamuddin Memon 
wrote:

> Instead of .trr file you can use .tpr and .xtc file
>
>
> On Wed, May 29, 2019, 10:25 PM Neena Susan Eappen <
> neena.susaneap...@mail.utoronto.ca> wrote:
>
>> Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr
>>
>> Specify 2 groups to analyze:
>>
>> Group 0 (System) has   130 elements
>>
>> Group 1 (Protein) has   130 elements
>>
>> Group 2 (Protein-H) has63 elements
>>
>> Group 3 (C-alpha) has11 elements
>>
>> Group 4 (Backbone) has34 elements
>>
>> Group 5 (MainChain) has47 elements
>>
>> Group 6 (MainChain+Cb) has58 elements
>>
>> Group 7 (MainChain+H) has58 elements
>>
>> Group 8 (SideChain) has72 elements
>>
>> Group 9 (SideChain-H) has16 elements
>>
>>
>> Select a group: 1 Selected 1: 'Protein'
>>
>> Select a group: 1 Selected 1: 'Protein'
>>
>> Output: Calculating hydrogen bonds in Protein (130 atoms)
>>
>> Found 13 donors and 25 acceptors
>>
>> trr version: GMX_trn_file (single precision)
>>
>> Reading frame   0 time0.000
>>
>> Will do grid-seach on 2374x2374x2374 grid, rcut=0.35
>>
>> Segmentation fault (core dumped)
>>
>> 
>> From: Neena Susan Eappen
>> Sent: Tuesday, May 28, 2019 11:31 PM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Segmentation fault, core dumped error
>>
>> Hello gromacs users,
>>
>> Is there a reason why segmentation fault appeared when gmx hbond command
>> was used?
>>
>> Thank you,
>> Neena
>>
>> 
>> From: Neena Susan Eappen
>> Sent: Friday, May 24, 2019 12:40 PM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] Segmentation fault, core dumped error
>>
>> Hello gromacs users,
>>
>> I got an error message when I used gmx hbond command: Segmentation fault,
>> core dumped. Shown below is my gmx version details (if that can point to my
>> problem). Any insight would be appreciated.
>>
>> GROMACS version:2018.4
>> Precision:  single
>> Memory model:   64 bit
>> MPI library:thread_mpi
>> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
>> GPU support:disabled
>> SIMD instructions:  AVX2_256
>> FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
>> RDTSCP usage:   enabled
>> TNG support:enabled
>> Hwloc support:  disabled
>> Tracing support:disabled
>> Built on:   2019-01-12 0:35
>> Built by:   name@HP-PC [CMAKE]<mailto:name@HP-PC%20[CMAKE]>
>> Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
>> Build CPU vendor:   Intel
>> Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
>> Build CPU family:   6   Model: 61   Stepping: 4
>> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma
>> htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse
>> rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>> C compiler: /usr/bin/cc GNU 7.3.0
>> C compiler flags:   march=core-AVX2 -O3 -DNDEBUG
>> -funroll-all-loops -fexcess-precision=fast
>> C++ compiler:   /usr/bin/c++ GNU 7.3.0
>> C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG
>> -funroll-all-loops -fexcess-precision=fast
>>
>> Thank you,
>> Neena
>> --
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Re: [gmx-users] Segmentation fault, core dumped error

[Najamuddin Memon]

Instead of .trr file you can use .tpr and .xtc file


On Wed, May 29, 2019, 10:25 PM Neena Susan Eappen <
neena.susaneap...@mail.utoronto.ca> wrote:

> Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr
>
> Specify 2 groups to analyze:
>
> Group 0 (System) has   130 elements
>
> Group 1 (Protein) has   130 elements
>
> Group 2 (Protein-H) has63 elements
>
> Group 3 (C-alpha) has11 elements
>
> Group 4 (Backbone) has34 elements
>
> Group 5 (MainChain) has47 elements
>
> Group 6 (MainChain+Cb) has58 elements
>
> Group 7 (MainChain+H) has58 elements
>
> Group 8 (SideChain) has72 elements
>
> Group 9 (SideChain-H) has16 elements
>
>
> Select a group: 1 Selected 1: 'Protein'
>
> Select a group: 1 Selected 1: 'Protein'
>
> Output: Calculating hydrogen bonds in Protein (130 atoms)
>
> Found 13 donors and 25 acceptors
>
> trr version: GMX_trn_file (single precision)
>
> Reading frame   0 time0.000
>
> Will do grid-seach on 2374x2374x2374 grid, rcut=0.35
>
> Segmentation fault (core dumped)
>
> 
> From: Neena Susan Eappen
> Sent: Tuesday, May 28, 2019 11:31 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Segmentation fault, core dumped error
>
> Hello gromacs users,
>
> Is there a reason why segmentation fault appeared when gmx hbond command
> was used?
>
> Thank you,
> Neena
>
> 
> From: Neena Susan Eappen
> Sent: Friday, May 24, 2019 12:40 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Segmentation fault, core dumped error
>
> Hello gromacs users,
>
> I got an error message when I used gmx hbond command: Segmentation fault,
> core dumped. Shown below is my gmx version details (if that can point to my
> problem). Any insight would be appreciated.
>
> GROMACS version:2018.4
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:disabled
> SIMD instructions:  AVX2_256
> FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
> RDTSCP usage:   enabled
> TNG support:enabled
> Hwloc support:  disabled
> Tracing support:disabled
> Built on:   2019-01-12 0:35
> Built by:   name@HP-PC [CMAKE]
> Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
> Build CPU vendor:   Intel
> Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
> Build CPU family:   6   Model: 61   Stepping: 4
> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /usr/bin/cc GNU 7.3.0
> C compiler flags:   march=core-AVX2 -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> C++ compiler:   /usr/bin/c++ GNU 7.3.0
> C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
>
> Thank you,
> Neena
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Re: [gmx-users] gmx hbond query

[Najamuddin Memon]

Make index of water mediated hydrogens and DNA bases so that DNA bases are
in separate group and water mediated hydrogens in separate group in drop
down menu

On Thu, May 9, 2019, 11:54 AM  wrote:

> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule. What extra flag should I use in gmx hbond command? Is
> there any other option to capture the water mediated Hbonds? Please
> suggest something.
> Sunipa Sarkar
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Re: [gmx-users] Membrane-protein Simulation

[Najamuddin Memon]

Yes it is normal to correct .xtc file through -pbc flag

On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in> wrote:

> Dear all,
>
> We are investigating the hydration dynamics of membrane proteins (AQP
> embedded in DPPC membrane). The topology and the mdp files for simulations
> was obtained from the MemprotMD database (mdp file:
> http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of
> simulation to 310 K since we are interested in the hydration dynamics at
> body temperature. After 100 ns simulations, we observe that the protein has
> drifted from the center of the bilayer to the periphery. There was no
> changes in the lipid layers. The apparent movement of the protein vanished
> after pbc correction was performed with centering the protein. Could you
> please advise if it is common to observe proteins drifting during the
> simulation and if it is fine to correct it with pbc correction?
>
> Thanks.
> --
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Re: [gmx-users] multiple replica trajectory analysis

[Najamuddin Memon]

When you are trying to join two .xtc files phosphorylated residues will be
broken. They remain intact when you generate the pdb files or any other
analysis.xvg from one and single .xtc file that you have suggested before
running md simulation

On Thu, May 2, 2019, 12:19 PM vijayakumar gosu 
wrote:

> Dear Gromacs users,
>
>
>
> I have simulated a phosphorylated protein with 3 replicas (for 300ns). I
> concatenated the three replicas (total 900ns) for the analysis
> (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include
> the 3 phospho residues. However when I analyzed each replica independently,
> protein considers all the residues including phospho residues. I am
> confused whether I am doing anything wrong when concatenating the
> trajectories. I performed analysis using 1_trj.tprfile from the first
> replica. Please someone suggest which .tprfile has to be used for analysis
> from 3 replicas. I have given a command below.
>
>
> echo 4 4 | gmx rms -f 1_2_3_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns
>
> Select group for output
>
> Group 0 ( System) has 43190 elements
>
> Group 1 (Protein) has  2927 elements
>
> Group 2 (  Protein-H) has  2302 elements
>
> Group 3 (C-alpha) has   292 elements
>
> Group 4 (   Backbone) has   876 elements
>
> Group 5 (  MainChain) has  1169 elements
>
> Group 6 (   MainChain+Cb) has  1443 elements
>
> Group 7 (MainChain+H) has  1454 elements
>
> Group 8 (  SideChain) has  1473 elements
>
> Group 9 (SideChain-H) has  1133 elements
>
> Group10 (Prot-Masses) has  2927 elements
>
> Group11 (non-Protein) has 40263 elements
>
> Group12 (  Other) has38 elements
>
> Group13 (T1P) has26 elements
>
> Group14 (S1P) has12 elements
>
> Group15 ( NA) has16 elements
>
> Group16 (  Water) has 40209 elements
>
> Group17 (SOL) has 40209 elements
>
> Group18 (  non-Water) has  2981 elements
>
> Group19 (Ion) has16 elements
>
> Group20 (T1P) has26 elements
>
> Group21 (S1P) has12 elements
>
> Group22 ( NA) has16 elements
>
> Group23 ( Water_and_ions) has 40225 elements
>
>
> If i check for independent replica, using the below command
>
> echo 4 4 | gmx rms –f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns
>
> Select group for output
>
> Group 0 ( System) has 43190 elements
>
> Group 1 (Protein) has  2965 elements
>
> Group 2 (  Protein-H) has  2334 elements
>
> Group 3 (C-alpha) has   295 elements
>
> Group 4 (   Backbone) has   885 elements
>
> Group 5 (  MainChain) has  1181 elements
>
> Group 6 (   MainChain+Cb) has  1458 elements
>
> Group 7 (MainChain+H) has  1469 elements
>
> Group 8 (  SideChain) has  1496 elements
>
> Group 9 (SideChain-H) has  1153 elements
>
> Group10 (Prot-Masses) has  2965 elements
>
> Group11 (non-Protein) has 40225 elements
>
> Group12 (  Other) has 40225 elements
>
> Group13 (SOL) has 40209 elements
>
> Group14 ( NA) has16 elements
>
> is it ok to make index file (protein+phosphoresidues) for analysis of the
> concatenated trajectory.
>
> Please advise me
>
> Thanks a lot
> Gosu
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Re: [gmx-users] In continuous I got another warning, could anyone help me?

[Najamuddin Memon]

Thirdly, change constraints=all bonds instead of h bond in nvt and npt.mdp
files

On Tue, Mar 5, 2019, 11:16 PM Najamuddin Memon 
wrote:

> Do nvt and npt equillibration for 1000 ps with nxtcout, etc values 500 in
> nvt.mdp and npt.mdp file.
> Secondly, this error can be removed by changing couple intramol=yes in
> mdout.mdp file or md.mdp file.
>
> On Tue, Mar 5, 2019, 10:31 PM banijamali_fs 
> wrote:
>
>> Hi there,
>>
>> Thanks for your response, but when I went to that link, it was said to
>> put -nt 1 in command line, so when I put this I get another warning that
>> is,
>>
>> Listed nonbonded interaction between particles 1 and 29
>> at distance 2.404 which is larger than the table limit 2.200 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the
>> table-extension
>> distance in the mdp file if you are really sure that is the reason.
>>
>> So what should I do with this?
>>
>> Do anyone knows what should I exactly do?
>> --
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>>
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>>
>
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Re: [gmx-users] In continuous I got another warning, could anyone help me?

[Najamuddin Memon]

Do nvt and npt equillibration for 1000 ps with nxtcout, etc values 500 in
nvt.mdp and npt.mdp file.
Secondly, this error can be removed by changing couple intramol=yes in
mdout.mdp file or md.mdp file.

On Tue, Mar 5, 2019, 10:31 PM banijamali_fs  wrote:

> Hi there,
>
> Thanks for your response, but when I went to that link, it was said to
> put -nt 1 in command line, so when I put this I get another warning that
> is,
>
> Listed nonbonded interaction between particles 1 and 29
> at distance 2.404 which is larger than the table limit 2.200 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the
> table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> So what should I do with this?
>
> Do anyone knows what should I exactly do?
> --
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Re: [gmx-users] Fwd: Phosphorylated serine and threonine residues (Gromacs MD)

[Najamuddin Memon]

Dear use 43a1 extended phosphorylated force field. Although phosphorylated
amino acids are not in the active site or not involved in the interaction
with ligand but in broad context these phosphorylated residues have impact
on structure of protein over the function of time


On Mon, Feb 11, 2019, 6:32 PM Swapnil Bhujbal  Dear all,
>
> I am working with a protein having phosphorylated serine and threonine
> residues. I will be performing ligand-protein MD. These phosphorylated
> amino acid residues are not located in the active site of protein.
> Should I just replace the phosphorylated serine and threonine residues with
> serine and threonine before MD preparations? Or shoild I ignore them
> because they will not be involved in any interactions with the ligand? Or
> do we have different force fields for the phosphorylated residues ?
>
> Your suggestions are highly appreciated.
>
> Thank you.
>
> Sincerely,
> Mr. Swapnil Bhujbal
> PhD Scholar,
> School of Medicine,
> Chosun University,
> South Korea.
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[gmx-users] Najam

[Najamuddin Memon]

I am working on MD simulation while using Gromacs. I want to simulate 
acetylated protein with DNA. Which type of force field I have to use that 
encompass both DNA and acetylated histones parameters. 

Regards 
Najam
QAU, Pakistan.


Sent from Mail for Windows 10

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