[gmx-users] New residue for custom capping

Simon Kit Sang Chu simoncks1994 at gmail.com
Fri May 12 09:05:02 CEST 2017

Hi everyone,

I am using a new forcefield which does not give proper neutral capping, but
requires me to create a custom made residue for that purpose. Specifically,
I want a NH2 cap instead of NH+.

I rename VAL1 into VAT1, update .hdb & .rtp. However, when I pdb2gmx -ter
to create a topology file (none cap for N-terminal, COO- cap for
C-terminal), the error warns missing hydrogen atom in GLY2. If I chose NH+
cap and COO- cap, the N+ occurs in GLY2 instead of VAT1. I believe the
capping option does not recognize the new residue VAT from the beginning.

Is there any file the capping code depends on, to add my new residue VAT?


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