On 4/1/15 4:27 PM, Alex wrote:
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. :)
Well, I already showed you the function to modify to change it to your heart's
desire ;)
-Justin
On Wed, Apr 1, 2015 at 2:18 PM, Justin Lemkul <[email protected]> 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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
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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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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