[gmx-users] extract subset from cpt?

[Roland Schulz]

On Thu, Aug 18, 2011 at 3:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>

Yes, one can only get coordinates and velocities. But as you said, it
doesn't make sense to get the full state.

Roland


>
> -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.
> >
> >     --
> >     ==================================================================
> >     Peter C. Lai                    | University of Alabama-Birmingham
> >     Programmer/Analyst              | BEC 257
> >     Genetics, Div. of Research      | 1150 10th Avenue South
> >     pcl at uab.edu <mailto:pcl at uab.edu>                     | Birmingham AL
> >     35294-4461
> >     (205) 690-0808 <tel:%28205%29%20690-0808>                        |
> >     ==================================================================
> >
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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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