[gmx-users] include a few .itp files

Алексей Раевский rayevsky85 at gmail.com
Sun Feb 6 20:57:14 CET 2011

I have some problems using ff_charmm27 ported in gromacs 4.5.3.
1) I want to build a topology of phosphorylated tyrosine in one
position of activated protein. I can make it with swissparam.ch server
(getting .itp) or by my hands. But the situation is complicated enough
for me, because of necessity to add some hydrogenes (to ester O in
phosphate group) to the structure from Marvel Sketch. In other case
server claimed the mol2 file is bad. So what to do? Add hydrogens to
this oxygenes or not? I'm not sure it is right... I think they must be
'free' from H...
2) I need to include several .itp (tyrosine-PO3 and ligand). Adding
strings "include..." before [molecule] section in the top of .top
And when I did grompp i've got an error invalid order [atomtype] for
the last itp. It isn't important which .itp is first, cause the
exchange of the strings order do nothing: just an error for the 'new'
last .itp

Thank you

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