[gmx-users] force field / parameters for NADH, FMN
jalemkul at vt.edu
Sun Nov 5 18:12:24 CET 2017
On 11/3/17 10:33 AM, Hermann, Johannes wrote:
> Hey Justin,
> thanks - again - for your reply!
> Now I get duplicated parameters warnings and errors:
> WARNING 1 [file fmn.prm, line 5]:
> Overriding Bond parameters.
> old: 0.1295 405848 0.1295
> new: CG2R64 NG2D1 1 0.14140000 255224.00
> ERROR 1 [file fmn.prm, line 35]:
> Encountered a second block of parameters for dihedral type 9 for the
> atoms, with either different parameters and/or the first block has
> multiple lines. This is not supported.
> I did *not* tick the "Include parameters that are already in CGenFF"
> on the webserver when generating the str file. I am using the newest
> version of cgenff_charmm2gmx.py. Do you have any hint for me?
Well, you've managed to stumble across a case where the version
difference *does* actually matter. Use whatever the existing parameters
are for the conflicting types, not the ones in your .str file. Your
parameters assume the interactions are unknown and is making a guess at
them; the ones in the CGenFF 4.0 parameter set have been specifically
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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