[gmx-users] could all-atom small molecule work with united atom biomemrane?

Yuhua Song yhsong at ccb.wustl.edu
Mon Feb 2 18:38:01 CET 2004

Dear Gromacs-mailing list and developer:

I am using the united atom force field ffgmx that addionally add some
biomembrane information ( got from Gromacs mailing list) to study
biomembrane, now, I intend to add an all-atom small molecule into the
system.  I had got many suggestion from mailing list about how to get the
all atom topology of small molecule using PDB2GMX using OPLSA force field.

I am wondering that if I get all atom topology of small molecule with
PDB2GMX using OPLSA force field, could the all atom small molecule work
together with the united atom Biomembrane which use ffgmx united atom force
field?  Because the ffgmx and oplsa has different *.atp, *.rtp definition,
the all atom topology of small molecule from oplsa, the united atom topology
of biomembrance from ffgmx will get into "doest not match" somehow?



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