[gmx-users] Write a pdb file after every ns of simulation

[MUSYOKA THOMMAS]

Thanks Tsjerk,
I have a 10 ns protein-ligand MD simulation and want to extract a pdb
structure (protein-ligand) at every nanosecond time point,

So I used the following command trjconv -f md_fit.xtc -s ../md.tpr -sep -dt
1000 -o out.pdb

and selected the protein | ligand group

However, when I open the output pdb files I am not getting the ligand.

What am I missing?

Thanks


On Wed, Apr 30, 2014 at 11:02 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Musyoka,
>
> Provided you saved enough:
>
> trjconv -dt 1000
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, Apr 30, 2014 at 9:46 AM, MUSYOKA THOMMAS <
> mutemibiochemistry at gmail.com> wrote:
>
> > Dear Users,
> > I want to write a pdb file after each ns of my 10 ns protein-ligand
> > trajectory
> > Which command do I use?
> > Thank you
> > --
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> --
> Tsjerk A. Wassenaar, Ph.D.
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