[gmx-users] New residue for custom capping

[Mark Abraham]

Hi,

Those define your residue, but do not classify it, so pdb2gmx doesn't know
that protein-specific termini are appropriate.

>From the link I provided: "Add your residue to residuetypes.dat with the
appropriate specification (Protein, DNA, Ion, etc)."

Mark

On Fri, May 12, 2017 at 9:39 AM Simon Kit Sang Chu <simoncks1994 at gmail.com>
wrote:

> 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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