Re: [gmx-users] phosphorylated protein parametrization

2017-12-07 Thread 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

Re: [gmx-users] phosphorylated protein parametrization

2017-12-07 Thread 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

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread R C Dash
; 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/ >

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread 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

Re: [gmx-users] (no subject)

2017-10-27 Thread 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

Re: [gmx-users] Fwd: Simulation of surfactant and water composition

2017-10-12 Thread 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

Re: [gmx-users] How to extend the protein simulation in Gromacs from 1 ns to 150 ns?

2017-10-12 Thread 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