[gmx-users] non-standard residues in pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 9 23:35:41 CEST 2009

Gard Nelson wrote:
> Hey everyone,
> I have a .pdb file that I need to convert to .gmx.  The tricky thing is 
> that the protein has a lipid bound to the N-terminus, which pdb2gmx 
> doesn't recognize.  The lipid is a myristic acid residue (14:0), and I 
> haven't been able to find it in any database.  What would be the most 
> straightforward way to get pdb2gmx to recognize this structure?  I plan 
> on using multiple monomers in the future, so I'd rather not manually 
> alter the .top file.  I've been looking at modifying the .rtp file to 
> include this residue, but then I'm wondering how to parameterize it.  If 
> anyone has any suggestions aobut any of this, I'd be really happy to 
> hear it.

If you want pdb2gmx to recognize it, then the .rtp is the only way to do it.  As 
for parameterization, see the standard advice:


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.  It's essentially the same amount of work to create an .itp file 
as it is to make an .rtp entry - the real work is in parameterization!


> Thanks,
> Gard
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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