[gmx-users] g_rama and NH2 problem

Weihua Guo whguo at midway.uchicago.edu
Fri Sep 17 18:17:40 CEST 2004


I have met some problem when using g_rama for my system. My system has two
peptides, both capped with ACE and NH2 groups and the force field is
OPLS. I have followed previous threads to solve the problem due to ACE,
but still have problem with NH2 group. It gave me an error message saying

Fatal error: Dihedral around 128,131 not found in topology

Atom 128 and 131 are O atom from last residue and one of the NH2 hydrogen
atom respectively (of the first peptide).

Here is part of the .gro file:

    8GLU      C  127   2.773   2.900   1.352
    8GLU      O  128   2.801   2.819   1.266
    9NH2      N  129   2.817   3.026   1.333
    9NH2     H1  130   2.785   3.084   1.408
    9NH2     H2  131   2.870   3.031   1.249

How can I get around this error?



Weihua Guo
Department of Chemistry
The University of Chicago
5735 S Ellis Ave 
Chicago, IL 60637

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