VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 20 2007 - 14:45:27 CST

On Tue, 20 Feb 2007, PREETA DATTA wrote:

PD> Hi Axel,
PD> Thanks for your reply.
PD> I tried running XLEAP with the CHARMM pdb and psf
PD> files for POPC, but obviously it cannot identify the
PD> different atoms.
PD> Can you tell me whether I can generate CHARMM
PD> coordinate/topology file with VMD?

VMD ships with psfgen. please see the manuals
(actually the membrane builder uses it implicitely).

these kind of questions to pop up recurringly,
please check out the tutorial manual on the VMD/NAMD
homepages and search the mailing list archives.

axel.

PD> I am thinking of another alternative, i.e. getting
PD> parameters for POPC in AMBER and using those along
PD> with CHARMM pdb to generate AMBER coordinate file.Is
PD> that possible?
PD>
PD>
PD>
PD> --- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
PD> wrote:
PD>
PD> > On Tue, 20 Feb 2007, PREETA DATTA wrote:
PD> >
PD> > PD> Hello,
PD> >
PD> >
PD> > preeta,
PD> >
PD> > please don't repost n+1 times. due to the ever
PD> > increasing amount of spam
PD> > and corresponding countermeasures, the turnaround
PD> > times are getting
PD> > higher. please wait a few hours until you assume
PD> > that your mail was lost
PD> > and that you may need to repost. thanks.
PD> >
PD> >
PD> > PD> I am working on bilayers and have newly
PD> > started using VMD.I am facing the following problem
PD> > :
PD> > PD>
PD> > PD> I have generated a POPC bilayer using
PD> > 'membrane' plugin in VMD.I have got the
PD> > corresponding .pdb and .psf files, using VMD.Those
PD> > files are CHARMM compatible.
PD> > PD> Now , I wish to run MD simulations for this
PD> > bilayer in AMBER using CHARMM forcefield.
PD> > PD> I cannot create the CHARMM coordinate and
PD> > topology files using VMD.
PD> >
PD> > VMD does not write AMBER style topology files. if
PD> > you want that, you
PD> > have to program it, sorry. i am wondering why you'd
PD> > want to do this, anyway.
PD> > to the best of my knowledge, urey-bradley support in
PD> > amber is experimental
PD> > and not compiled in by default.
PD> >
PD> > shouldn't you be using NAMD anyways?? ;-)
PD> >
PD> > axel.
PD> >
PD> >
PD> > PD>
PD> > PD> Is it possible to create AMBER compatible
PD> > topology and coordinate files (from these pdb and
PD> > psf files I have) ?
PD> > PD>
PD> > PD> Any help in this regard would be highly
PD> > appreciated.
PD> > PD>
PD> > PD> Thanks,
PD> > PD> Preeta
PD> > PD> (Project Assisstant,
PD> > PD> Indian Institute of Science)
PD> > PD>
PD> > PD>
PD> > PD> ---------------------------------
PD> > PD> Need Mail bonding?
PD> > PD> Go to the Yahoo! Mail Q&A for great tips from
PD> > Yahoo! Answers users.
PD> >
PD> > --
PD> >
PD> =======================================================================
PD> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
PD> > http://www.cmm.upenn.edu
PD> > Center for Molecular Modeling -- University
PD> > of Pennsylvania
PD> > Department of Chemistry, 231 S.34th Street,
PD> > Philadelphia, PA 19104-6323
PD> > tel: 1-215-898-1582, fax: 1-215-573-6233,
PD> > office-tel: 1-215-898-5425
PD> >
PD> =======================================================================
PD> > If you make something idiot-proof, the universe
PD> > creates a better idiot.
PD> >
PD> >
PD>
PD>
PD>
PD>
PD> ____________________________________________________________________________________
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PD> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.