[gmx-users] protein drug tutorial

John Kerrigan kerrigje at umdnj.edu
Wed May 14 19:01:02 CEST 2003


I trust you added your drug coordinates to the end of your overall protein
gro file.  There are a couple of edits that you must perform to satisfy

1.  Re-number the atoms in the drug portion you added so they
continue from where the protein left off.  In other words, the # sequence
cannot be interrupted then restarted again (1, 2, 3, ... 1, 2, 3 is not
allowed).  There cannot be any numbers missing in the sequence, either.
2.  Revise the total number of atoms at the beginning of the file so it
reflects the new total (accounting for the # of drug atoms).
3.  You may need to revise the residue # so that it is consecutive with
the protein as well.  

Remember to include the drg.itp file in your topology file.  In addition
remember to include ions.itp if you add ions later on.


John E. Kerrigan, Ph.D.
Robert Wood Johnson Medical School
675 Hoes Lane
Piscataway, NJ 08854  USA

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

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