[gmx-users] grompp: unknown bond_atomtype

[Justin Lemkul]

On 4/1/15 2:03 PM, Alex wrote:
> I am working with a local copy of oplsaa.ff where I have defined a set of
> custom atom types in atomname2type.n2t and added the bond and angle
> parameters into ffbonded. x2top creates the topology without issues, but
> grompp reports a fatal error (see subject).
> The particular type it complains about is actually opls_335. Gromacs v.
> 4.6-beta3. Any ideas?
>

Don't use beta versions, especially ancient ones.

The problem is related to a translated type; note that in ffnonbonded.itp the 
second column is an atom type that is used in ffbonded.itp.  These are different 
from the nonbonded types, but since there are fewer bonded types to cover the 
parameters, these are used to remove redundancy.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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