[gmx-users] Improper Dihedrals

[Dallas Warren]

David,

>based on atomtype.
>Check the type your atoms have in the [ atoms ] section

Actually, that isn't quite what I am asking.

In the bon.itp file for the force field, there are two constants defined 
for i and l  These are some how put together to form an improper dihedral 
for i, j, k, l.  In the case of an amide bond (with ffgmx), you have atom 
types CH2, C, OM and N.  Therefore, which improper dihedrals have to be 
defined in ffgmxbon.itp to form the final description of it?  CH2 - N, CH2 
- OM and N - OM?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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