VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 20 2007 - 09:05:44 CST

On Tue, 20 Feb 2007, PREETA DATTA wrote:

PD> Hello,

preeta,

please don't repost n+1 times. due to the ever increasing amount of spam
and corresponding countermeasures, the turnaround times are getting
higher. please wait a few hours until you assume that your mail was lost
and that you may need to repost. thanks.

PD> I am working on bilayers and have newly started using VMD.I am facing the following problem :
PD>
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?? ;-)

axel.

PD>
PD> Is it possible to create AMBER compatible topology and coordinate files (from these pdb and psf files I have) ?
PD>
PD> Any help in this regard would be highly appreciated.
PD>
PD> Thanks,
PD> Preeta
PD> (Project Assisstant,
PD> Indian Institute of Science)
PD>
PD>
PD> ---------------------------------
PD> Need Mail bonding?
PD> Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.