[gmx-users] regarding SwissParam topology

soumadwip ghosh soumadwipghosh at gmail.com
Wed Jun 10 15:22:49 CEST 2015


Thanks Justin,
                    actually I did look into what you suggested. I
made a carbon nanotube topology with the help of pbd2gmx. Now, the
atomtypes specified in the .rtp file was CA as it is aromatic carbon
atoms. Then I looked into the cnt.itp file and the kb, force constant
and other terms in it were missing and proceeding with it made grompp
complain about 'missing parameters in the itp file'. Hence I looked
into ffbonded and ffnonbonded.itp files and manually filled the
missing columns in the cnt.itp. It was a trivial job as the cnt was
constituted with similar carbon atoms and terminal hydrogens. The
interaction of this nanotube with a sigle stranded DNA was as
expected. There was helical wrapping and non-bonding interactions
could be captured perfectly using this model. However, for a similar
system like fullerene interactions are not arising with DNA when an
alternative SwissParam topology is used.

I am thinking of changing those atomtypes from CB to CA in
fullerene.itp file and have a trial whether the interaction patterns
are changing or not. I am quite sure if I generate the topology by
pdb2gmx and then fill up the missing parts from the forcefield files,
the desired interaction would arise because it happened for the cnt
case and anyways making an rtp and topology for a small molecule like
fullerene wont be an issue. I was just wondering why this .itp from
SwissParam behaves so weirdly.

I would love to hear fro you.

Regards,
Soumadwip Ghosh
IITB
India


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