[gmx-users] extract subset from cpt?
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 18 21:02:29 CEST 2011
Roland Schulz wrote:
> 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.
> 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
> 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
> (205) 690-0808 <tel:%28205%29%20690-0808> |
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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