[gmx-users] non-standard residues in pdb2gmx

Gard Nelson gardnersnake23 at gmail.com
Tue Jun 9 23:28:03 CEST 2009

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.

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