So to obtain the parameters(e.g. bonds) in topology file,
1, read bond atoms in .top (e.g. 1 2)
2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
oplsaa_236)
3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)
4, check parameters in ffoplsaabon.itp
Is that right? why it comes to such complex in GMX?
thanks
Qiang
Mark Abraham wrote:
friendli wrote:
In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type
opls_235 and opls_236.
While in oplsaanb.itp, the atom type opls_235 and opls_236
corresponds to atom "name"(as display in titles in oplsaanb.itp) C
and O.
why there are two different "name"s for the same atom? what is the
difference?
Different force fields use the machinery differently, but I can't
think of a purpose for the atom name field in the parameter .itp file
if there is a separate atom type.
The purpose of atom names, residue names and residue numbering in a
pre-pdb2gmx structure file is to look up the right atom types in the
.rtp file and write them to the .top file. The purpose of the atom
types in the .top file is to look up the right parameters in the .itp
file when running grompp. At that point, atom names are probably just
for user convenience.
Mark
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