Nguyen Hoang Phuong wrote:
Is pdb2gmx recognising the N-terminal residue as PRO?
I think so. However in my case pdb2gmx does not read the entry PRO-NH in
the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat
pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works
for me now.
This immediately indicates that there is nothing wrong with the format
(and functionality) of the [ PRO-NH ] section, and suggests that the
problem is pdb2gmx recognising the applicability of this capping to your
N-terminal residue. I suggest stripping off any capping on the PRO in
your input file, and carefully comparing the atoms with those in
ffG43a1.rtp for PRO. You might also try an input of a plain PRO amino acid.
Mark
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