[gmx-users] force field / parameters for NADH, FMN

[Justin Lemkul]

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 
> 405848
>   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 
> same
>   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 
optimized.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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