Re: [gmx-users] phosphorylated protein parametrization

[R C Dash]

https://www.swisssidechain.ch/browse/family/table.php?family=all. Here you
can get all the gromaccs topology file  for phosphorylated THR ( Charmms FF)

On Thu, Dec 7, 2017 at 12:00 PM,  wrote:

> Hi folks,
> what do I need to do to run pdb2gmx with a protein pdb file that contains
> phosphorylated THR labeled as THP? I see several solutions but no of them
> look elegant. Does anybody have any experience with this,
> Thanks for any advice,
> Cheers,
> www.svedruziclab.com
>
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Re: [gmx-users] phosphorylated protein parametrization

[R C Dash]

Hi,
 Which force field you want to use for parameterisation ?

On Thu, Dec 7, 2017 at 12:00 PM,  wrote:

> Hi folks,
> what do I need to do to run pdb2gmx with a protein pdb file that contains
> phosphorylated THR labeled as THP? I see several solutions but no of them
> look elegant. Does anybody have any experience with this,
> Thanks for any advice,
> Cheers,
> www.svedruziclab.com
>
> --
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Re: [gmx-users] itp file for aminoacids

[R C Dash]

can you please upload your PDB file?

On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani <rose.rhm...@gmail.com>
wrote:

> if it is included,so why AMBER doesnt identify amino acids like THR?
> error is such 'X' residuetype is not found in residue topology
> database?
> i dont know what is the problem?
>
> thanks for your attention
>
> On Mon, Oct 30, 2017 at 6:25 PM, R C Dash <rcdash0...@gmail.com> wrote:
>
> > use https://atb.uq.edu.au/index.py /
> > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or
> > http://swissparam.ch/
> > or http://vienna-ptm.univie.ac.at/  for .itp file
> > All amino acids are identified bybby AMBER force field. If you there is
> > some modification like methylated lysine you have to creat a lib file and
> > use it in tleap AMBERTools.
> >
> > On Mon, Oct 30, 2017 at 10:48 AM, Tasneem Kausar <
> > tasneemkausa...@gmail.com>
> > wrote:
> >
> > > You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs
> > does
> > > the job of making itp.
> > >
> > > <https://www.avast.com/sig-email?utm_medium=email_
> > > source=link_campaign=sig-email_content=webmail>
> > > Virus-free.
> > > www.avast.com
> > > <https://www.avast.com/sig-email?utm_medium=email_
> > > source=link_campaign=sig-email_content=webmail>
> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > >
> > > On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani <rose.rhm...@gmail.com>
> > > wrote:
> > >
> > > > hello
> > > >
> > > > how can i make an .itp file for amino acids?
> > > > which amino acids is identified in AMBER forcefield?
> > > > --
> > > > Gromacs Users mailing list
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Re: [gmx-users] itp file for aminoacids

[R C Dash]

use https://atb.uq.edu.au/index.py /
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or http://swissparam.ch/
or http://vienna-ptm.univie.ac.at/  for .itp file
All amino acids are identified bybby AMBER force field. If you there is
some modification like methylated lysine you have to creat a lib file and
use it in tleap AMBERTools.

On Mon, Oct 30, 2017 at 10:48 AM, Tasneem Kausar 
wrote:

> You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs does
> the job of making itp.
>
>  source=link_campaign=sig-email_content=webmail>
> Virus-free.
> www.avast.com
>  source=link_campaign=sig-email_content=webmail>
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani 
> wrote:
>
> > hello
> >
> > how can i make an .itp file for amino acids?
> > which amino acids is identified in AMBER forcefield?
> > --
> > Gromacs Users mailing list
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> >
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Re: [gmx-users] (no subject)

[R C Dash]

use trjconv command with nojump option to center all the peptide. Use the
starting structure as the starting configuration.

regards,
RC Dash

On Fri, Oct 27, 2017 at 5:51 AM, saranya  wrote:

> Dear Users,
> I have done a simulation of Aggregated amyloid beta peptide for 100ns. The
> pdb structure choosen for my work is 1IYT, which has several (10) model
> structures, but i have choosen only 4 structure for my simulation. The
> problem is after production, if i check the final .gro files of md instead
> of 4 peptide structure i got only a single peptide structure. What is the
> reason for getting this result?
>
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
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Re: [gmx-users] Fwd: Simulation of surfactant and water composition

[R C Dash]

Use packmol software for system generation, save it in PDB file and then
use appropriate force field .

On Thu, Oct 12, 2017 at 8:01 AM, Amali Guruge  wrote:

> -- Forwarded message --
> From: 
> Date: Thu, Oct 12, 2017 at 10:11 PM
> Subject: Simulation of surfactant and water composition
> To: amaligg2...@gmail.com
>
>
> You are not allowed to post to this mailing list, and your message has
> been automatically rejected.  If you think that your messages are
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>
>
> -- Forwarded message --
> From: Amali Guruge 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc:
> Bcc:
> Date: Thu, 12 Oct 2017 22:11:11 +1100
> Subject: Simulation of surfactant and water composition
> Dear Gromacs users,
>
> I want to model a system which contains surfactant molecules and water
> molecules. I also want to model the system with w/w 15% surfactant/water
> composition. Could you please guide me to model the system and do the
> simulation using Gromacs software. Appreciate, if anyone can give a
> tutorial to do the simulation in step by step.
>
> Thank you.
>
> Sincerely,
> A Guruge
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Re: [gmx-users] How to extend the protein simulation in Gromacs from 1 ns to 150 ns?

[R C Dash]

As you already run 1ns molecular dynamics now you have md.tpr, md.cpt files
in your working directory

You need to creat a new tpr file (newmd.tpr) from previous md.tpr file

tpbconv -s md.tpr -extend  149000 -o newmd.tpr

149000 is ps
then use
mdrun -s newmd.tpr -cpi previous.cpt



On Thu, Oct 12, 2017 at 11:24 AM, Rahma Dahmani 
wrote:

> Hi,
> i am a beginner with Gromacs and i have run the simulation using Gromacs
> forcefield for 1000 ps* (1ns)* . Now I want to extend it to *150 ns*. How
> should I proceed?
> should i change the md.mdp file ?? actually i am using the defaul mdp file
> in gromacs tutorial :
> integrator  = md; leap-frog integrator
> nsteps  = 50; 2 * 50 = 1000 ps, 1 ns
> dt = 0.002   ; 2 f
>
> so what should i change exactly??
> can anyone help me please,
>
> Thank you
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
> Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
> Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
> Tunisie Tél: (+216) 28151042*
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