[gmx-users] New residue for custom capping

Mark Abraham mark.j.abraham at gmail.com
Fri May 12 09:32:09 CEST 2017


I suspect you need to add your residue to the class of Protein residues,


On Fri, May 12, 2017 at 9:05 AM Simon Kit Sang Chu <simoncks1994 at gmail.com>

> 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
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