[gmx-users] New residue for custom capping

[Simon Kit Sang Chu]

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?

Regards,
Simon