[gmx-users] extract subset from cpt?

[Justin A. Lemkul]

Roland Schulz wrote:
> Hi,
> 
> you can use trjconv for that (or editconf). You probably would want to 
> add some waters though.
> 

For trjconv, you can get a coordinate file, but not a .cpt; editconf throws a 
fatal error (unless I'm using it wrong, but I tried -f state.cpt).  If you try 
to output a .cpt from trjconv, it gives you file.cpt.xtc.  Is there some other 
way to preserve a state that's not given in the documentation?  You can write a 
.trr file, but that only gives you velocities.

-Justin

> Roland
> 
> On Thu, Aug 18, 2011 at 2:50 PM, Peter C. Lai <pcl at uab.edu 
> <mailto:pcl at uab.edu>> wrote:
> 
>     Is there anyway I can extract a subset of atoms from a cpt file,
>     like I can
>     with trjconv operating on a traj file? I want to remove a ligand and
>     still
>     keep all the remainder of the state information, so I can feed this back
>     into grompp with a modified topology and "continue" a run without
>     the ligand.
> 
>     --
>     ==================================================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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