[gmx-users] Unknown bond_atomtype

Nash, Anthony a.nash at ucl.ac.uk
Wed Feb 17 23:43:45 CET 2016

Thanks Justin,

I think that¹s everything I need to know.

Kind regards

Dr Anthony Nash
Department of Chemistry
University College London

On 17/02/2016 22:18, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:

>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 I¹ve sorted out
>> ffnonbonded [atomtypes], all that remains are some missing angle terms.
>> 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
>> 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 aren¹t 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? I¹m unsure what ³-C²
>> 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
>CGLY, ignoring the intervening residue, you probably either haven't set
>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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