On 6/9/12 8:31 AM, ramaraju801 wrote:
correction i added O2 atom to atomtypes.atp file
The atomtypes.atp file is only used by pdb2gmx to make sure it can write certain
atom types. If you're introducing a new atom type, its parameters need to go in
ffnonbonded.itp, and if it is involved in bonded interactions, those need to go
in ffbonded.itp. Before doing all that, you should determine whether all that
effort is needed. Based on the information at hand, I am still not clear on why
you think the addition is necessary.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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