[gmx-users] pdb2gmx with CHARMM-GUI output

Lewis J Martin lewis.martin44 at gmail.com
Thu Mar 22 00:18:34 CET 2018


I'd like to use pdb2gmx, mainly to add virtual sites to an existing 
system, either pre-equilibrated (in CHARMM) or a new system from 
CHARMM-GUI. Is pdb2gmx suitable for this? The issue Im coming across is 
that, choosing the CHARMM27 forcefield, the POPC lipids have a different 
naming convention and they aren't recognised. I could change the names 
in the PDB to match the lipids.rtp that gromacs uses, but the order of 
the atoms is also changed and there doesn't appear to be a logical 
(easy) way to match them up.

So - has anyone used pdb2gmx with CHARMM-GUI membrane outputs? Is there 
another way to add virtual sites? Hydrogen mass repartitioning will do 
in a pinch.



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