[gmx-users] include a few .itp files

[Justin A. Lemkul]

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

-- 
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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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