Oguz, in case you want to try the psfgen patch, it is now available for download on our group website at http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen
<http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen>Roland On Thu, Sep 30, 2010 at 7:28 PM, Roland Schulz <[email protected]> wrote: > Oguz, > > On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak <[email protected]>wrote: > >> Dear Dr. Roland Schulz, >> >> >> >> Thank you very much for your attention. I would like to have a copy of >> patch that generates gromacs topology from psf file. And could you please >> explain how to use this patch in detail ? Because I have no information on >> Pär's scripts. >> > Do you have standard CHARMM or Amber FF? Than you don't need to convert the > FF because it is already part of GROMACS. > > >> >> I think, In order to continue a NAMD simulation in Gromacs I should first >> save the last coordinates (.coor file in namd ) as a pdb file and convert it >> into gro file . But there are many ways to get a gro file >> > no you don't need to convert the coordinate file or get the last frame. > >> >> >> - using pdb2gmx ( but I should choose the force field in gromacs. This may >> be a problem. ) By the way, I changed CHARMM force field and use Amber type >> force field in NAMD. >> > Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a > standard molecule (e.g. protein), it will be much easier to just use pdb2gmx > to generate the topology. > > >> Could you share your ideas about this process ? What should I do ? >> > You would just do everything the same way as setting up a new simulation > and use the last frame as starting structure. Make sure you use a structure > which includes both coordinates and velocities. > >> Is there a way to get a tpr file from NAMD files? >> > No. Not automatically. You need to get all the input files (grompp.mdp, > topol.top, conf.gro) and then run grompp to generate your tpr. > > Roland > >> >> >> >> >> Kind regards. >> >> >> >> >> >> Oguz GURBULAK Ph.D. Student >> Ege University - Faculty of Science >> Department of Physics >> Branch of Atomic and Molecular Physics >> >> >> >> >> >> > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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