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
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
; 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/
>
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
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
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
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