[gmx-users] New residue in FF does not bond to others.

Dawid das addiw7 at googlemail.com
Fri Aug 8 20:39:20 CEST 2014

2014-08-08 15:48 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

> The problem is in atom naming.  You have used MN1 and MC3 for the
> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes here,
> because Phe-65 tries to make a bond to the +N atom, which it does not find
> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you rename
> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.

OK, I see your point but if I do as you suggest how will I specify
nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
atoms have different  vdW and electrostatic parameters than N and C atoms,

> If there are still missing parameters for interactions, you'll have to
> figure that out.  There are several missing inter-residue angles and
> dihedrals in your .rtp entry for CH6.

Do you mean those which I stated above?

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