VMD-L Mailing List

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Oct 02 2008 - 22:57:47 CDT

 I am little confused!! i think parameter file is not residue
 specific and hence if I can submit right 'type' of
 atoms in the file whose topology file is otherway running
 fine, it should work fine!!
 in my case, i have generated the topology file and solvated
 it to the water and upto that it is working fine. but given
 that i am not getting the right type of atom for tha
 non-ring N, it is giving some error at the time of MD
 
 
 --
 Rudra
 JRF; SNBNCBS
 http://www.bose.res.in/~rudra
 
 A bus station is where a bus stops. A train station is
 where a train
 stops. On my desk I have a work station.
 
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 Why?See:
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>
> --- On Thu, 2/10/08, Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> > From: Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu>
> > Subject: Re: vmd-l: atom type
> > To: "Rudra Banerjee"
> <bnrj.rudra_at_yahoo.com>
> > Cc: "VMD Mailing List"
> <vmd-l_at_ks.uiuc.edu>, "John Stone"
> <johns_at_ks.uiuc.edu>
> > Date: Thursday, 2 October, 2008, 11:46 PM
> > On Thu, 2 Oct 2008, Rudra Banerjee wrote:
> >
> > RB> no no...you misunderstood my question. I was
> not
> > seeking help on
> > RB> nomenclature of atom. rather i need to specify
> the
> > atom type of the
> > RB> said atoms so that there is bond given in
> parameter
> > file.
> >
> > as has been pointed out several times before.
> >
> > if you want to use CHARMM parameters, you have to have
> a
> > _proper_
> > parameter file with the corresponding topology _and_
> > parameters
> > for this specific residue. that will take care of
> bonding
> > as well.
> >
> > if you don't have this - and that seems to be the
> case
> > - you either
> > have to use a different force field that is supposed
> to be
> > more
> > "portable" (with the risk of being less
> accurate)
> > or generate the
> > missing parameters for yourself following the
> instructions
> > of the
> > publications on CHARMM force field parameterization.
> the
> > latter
> > is a non-trivial task except for small modifications
> to
> > existing
> > topologies, and - of course - requires that you know
> the
> > chemistry
> > of your compound well.
> >
> > cheers,
> > axel.
> >
> > RB>
> > RB>
> > RB>
> >
> > --
> >
> =======================================================================
> > 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.
>
>
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