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

[Hermann, Johannes]

Hi Justin,

just for testing, I applied cgenff_charmm2gmx.py with 
charmm36-nov2016.ff as it has the same CGenFF version:

--Version of CGenFF detected in 
/usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc 
: 3.0.1

But I still get the same warnings and errors.

Would you still recommend me to use the existing parameters and delete 
the respective lines from the str file?

Thank you in advance!

All the best

Johannes


On 05.11.2017 18:12, Justin Lemkul wrote:
>
>
> 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
>

-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de
http://www.biovt.mw.tum.de/