.rtp [bonds] requires atom names (because that's all that can be
reliably deduced from the coordinate file input)
.itp/.top [bonds] requires atom numbers (because prior sanity-ization
is assumed) to look up the atom types to look up the interaction
parameters
... and different force fields have sl
On 8/27/13 12:30 PM, Valentina wrote:
Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.
I have a few atom types and a few atoms per each atom type.
So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!
*S
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