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 <p...@uab.edu <mailto:p...@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
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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