[gmx-users] problem in energy minimisation during inflategro process.

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 14 08:33:35 CEST 2009


In addition to Mark's comments:

> ; Include chain topologies
> #include "rr1_A.itp"
> #include "rr1_B.itp"
> ; Include position restrain protein
> #include "rr1_A_pr.itp"
> #include "rr1_B_pr.itp"
> #endif

This is rubbish. Position restraints are defined as part of molecule
types. You can't include them outside the scope of a [ molecule_type ]
block. You'll get the 'invalid order of directives' error for that.
You have to include the position restraint include files in the
respective molecule definition include files. Understanding how
topologies and coordinates are put together is vital when doing
anything already slightly out of the ordinary.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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