[gmx-users] Unknown bond_atomtype

Justin Lemkul jalemkul at vt.edu
Wed Feb 17 23:18:43 CET 2016

On 2/17/16 5:11 PM, Nash, Anthony wrote:
> Hi,
> Thanks for the information, Mark. I fully parameterised the bonded terms
> using QM data and some software I wrote. Now that I’ve sorted out
> ffnonbonded [atomtypes], all that remains are some missing angle terms. I
> want to have the forcefield files correct so an MD simulation can be
> generated with very little changes to the topol file after running
> pdb2gmx. I do have a couple of questions that I hope you could help me
> with.
> 1) For grompp to compile successfully, must every molecule/residue have a
> complete set of dihedral angle force constants?

grompp will complain about any missing parameters, triggering a failure.

> 2) It appears as though the residue to residue bond connectivity in my
> force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
> bonded term is added to the topol for the C in NGLY to the N in CGLY. To
> avoid this must I add an entry such as -C N in the [ bonds ] section of
> the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
> means.

- indicates an atom in the previous residue, + means in the next residue.  So -C 
is the C in the previous residue.  If you're getting bonds between NGLY and 
CGLY, ignoring the intervening residue, you probably either haven't set your 
modified residue as Protein in residuetypes.dat or it doesn't have a C (which it 
should, if it's an amino acid.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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