[gmx-users] New residue for custom capping

[Simon Kit Sang Chu]

Mark,

Thanks Mark! Indeed it was the problem. I forgot to update residuetypes.dat.

Regards,
Simon

2017-05-12 15:46 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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