From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Oct 02 2008 - 13:16:47 CDT

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>

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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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