Алексей Раевский wrote:
Hi.
I have some problems using ff_charmm27 ported in gromacs 4.5.3.
The CHARMM ports are no longer necessary; CHARMM27 is incorporated into Gromacs
4.5.3 by default.
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...
You should base this decision on the pKa values of the phosphate and the
conditions you want to model.
2) I need to include several .itp (tyrosine-PO3 and ligand). Adding
strings "include..." before [molecule] section in the top of .top
file.
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
Presumably the tyrosine is incorporated into the backbone of your protein, is it
not? If it is a part of the protein, you cannot #include it as an .itp file.
You have to introduce the building block into the force field .rtp file (as well
the .hdb file, and maybe a few more, depending on your needs):
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
In any case, the topology format is quite sensitive to the order in which
molecules are introduced. If you're getting fatal errors, you're #including
things in the wrong order.
-Justin
Thank you
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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