[gmx-users] New residue for custom capping

[Simon Kit Sang Chu]

Dear Mark,

Thanks for your prompt reply. I have already updated my .rtp and .hdb for
my new residue. Would you mind to suggest which file I am missing?

I am happy to provide relevant parts of .rtp and .hdb if necessary.

Regards,
Simon

2017-05-12 15:31 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> I suspect you need to add your residue to the class of Protein residues,
> per
> http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field
>
> Mark
>
> On Fri, May 12, 2017 at 9:05 AM Simon Kit Sang Chu <simoncks1994 at gmail.com
> >
> wrote:
>
> > 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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