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

[Erik Marklund]

Hi,

What were your xtc groups in the map file? Perhaps you didn't include the ligand.

Yours,
Erik


On 30 Apr 2014, at 10:42, MUSYOKA THOMMAS <mutemibiochemistry at gmail.com> wrote:

> 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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