On Thu, Aug 18, 2011 at 3:02 PM, Justin A. Lemkul <jalem...@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 <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. > > > > -- > > ================================================================== > > Peter C. Lai | University of Alabama-Birmingham > > Programmer/Analyst | BEC 257 > > Genetics, Div. of Research | 1150 10th Avenue South > > p...@uab.edu <mailto:p...@uab.edu> | Birmingham AL > > 35294-4461 > > (205) 690-0808 <tel:%28205%29%20690-0808> | > > ================================================================== > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > <mailto:gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org > > <mailto:gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > -- > > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov < > http://cmb.ornl.gov> > > 865-241-1537, ORNL PO BOX 2008 MS6309 > > > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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