From: Axel Kohlmeyer (
Date: Tue Feb 20 2007 - 09:05:44 CST

On Tue, 20 Feb 2007, PREETA DATTA wrote:

PD> Hello,


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PD> I am working on bilayers and have newly started using VMD.I am facing the following problem :
PD> I have generated a POPC bilayer using 'membrane' plugin in VMD.I have got the corresponding .pdb and .psf files, using VMD.Those files are CHARMM compatible.
PD> Now , I wish to run MD simulations for this bilayer in AMBER using CHARMM forcefield.
PD> I cannot create the CHARMM coordinate and topology files using VMD.

VMD does not write AMBER style topology files. if you want that, you
have to program it, sorry. i am wondering why you'd want to do this, anyway.
to the best of my knowledge, urey-bradley support in amber is experimental
and not compiled in by default.

shouldn't you be using NAMD anyways?? ;-)


PD> Is it possible to create AMBER compatible topology and coordinate files (from these pdb and psf files I have) ?
PD> Any help in this regard would be highly appreciated.
PD> Thanks,
PD> Preeta
PD> (Project Assisstant,
PD> Indian Institute of Science)
PD> ---------------------------------
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Axel Kohlmeyer
   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.