[gmx-users] Re: Cofactor - Coenzyme - Enzyme Complex

[John Kerrigan]

Yes, you must be sure that the name given to the drug residue in drg.itp is
identical in the pdb file.  I forgot to include this in the tutorial in my
rush to prepare it for a course.  In a class setting, I can fill in the gaps
easily for students.  I will correct this omission and refine the tutorial
when I have some inkling of time this spring/summer ;)

There are topologies for the more common co-factors already available in the
gromacs forcefields.  If your co-factor matches one already in the
forcefield, just change the residue name in your pdb file so that it matches
the name used in the FF topology (see the appropriate ff*.rtp file in
~/share/top).

John

*******************************************************
John E. Kerrigan, Ph.D.
Computational Biologist

Adjunct Associate Professor
Dept. of Pharmacology

Academic Computing Services
RWJMS-Univ. of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

(732) 235-4473  phone
(732) 235-5252  fax

http://www2.umdnj.edu/~kerrigje
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