VMD-L Mailing List

From: PREETA DATTA (preita_datta_at_yahoo.com)
Date: Tue Feb 20 2007 - 14:30:11 CST

Hi Axel,
Thanks for your reply.
I tried running XLEAP with the CHARMM pdb and psf
files for POPC, but obviously it cannot identify the
different atoms.
Can you tell me whether I can generate CHARMM
coordinate/topology file with VMD?
I am thinking of another alternative, i.e. getting
parameters for POPC in AMBER and using those along
with CHARMM pdb to generate AMBER coordinate file.Is
that possible?

--- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
wrote:

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

 
____________________________________________________________________________________
Looking for earth-friendly autos?
Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.
http://autos.yahoo.com/green_center/