[gmx-users] non-standard residues in pdb2gmx

[Tsjerk Wassenaar]

Hi,

> What might be even easier is to create an .itp file for myristic acid, so
> you can #include "myristic.itp" in any topology that needs it.  That way you
> don't have to mess with .rtp files, or run pdb2gmx for every system that
> contains myristic acid.

But this doesn't help when it has to be bound to the protein. The bond
(angle, dihedral, etc) has to be set and on top of that the myristic
acid moiety has to be part of the same [ moleculetype ] definition,
including consistent numbering. You can't do it with an #include. You
have to have a .rtp entry and edit the file specbond.dat
(http://oldwiki.gromacs.org/index.php/specbond.dat).

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623