[gmx-users] grompp: unknown bond_atomtype
nedomacho at gmail.com
Wed Apr 1 22:27:16 CEST 2015
I think I solved it already, thanks. Entirely due to horrible mess created
by the necessity to create custom atom types. I wish you guys could make
the bond length tolerance an input to x2top, I really do. :)
On Wed, Apr 1, 2015 at 2:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 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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