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

[Hermann, Johannes]

Dear Justin, dear all,

thank you for your reply. I will test the web server when I have managed 
to generate the mol2 file for FMN.

I had a look in the rtp file of charmm36 ff and I detected that there 
are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code 
for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. 
NADH. However, both NAI and NADH in the rtp file have only 71 atoms, 
while they should have 73. Hence, if I am not mistaken, NAI and NADH are 
both NAD (not NADH or NAD+).

Has anyone who is reading this a ff field which he can send me? This 
would save me a lot of time.

Thanks in advance!

All the best

Johannes


On 30.10.2017 16:14, Justin Lemkul wrote:
>
>
> On 10/30/17 10:58 AM, Hermann, Johannes wrote:
>> Dear all,
>>
>> I want to simulate a complex consisting of a protein, FMN, and NADH. 
>> I have two problems/questions:
>>
>> 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for 
>> NADH are present. But apparently I am using a wrong atom naming 
>> convention (I copied / pasted NADH from a pdb entry):
>>
>> Fatal error:
>> Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms
>> while sorting atoms.
>>
>> How can I generate a appropriate input file for gromacs gmx2pdb?
>>
>
> Make the PDB file atom names match those of the .rtp entry. It's a bit 
> awkward but everyone seems to have a different convention for naming 
> cofactor atoms.
>
>> 2) I did not find FMN in the charmm36 force field. Can some recommend 
>> me a program to generate a parameter file? And how to proceed with it?
>>
>
> If it's not in CHARMM, use CGenFF. There's a web server that will 
> parametrize it (cgenff.paramchem.org) and tell you how good the 
> topology is so you can decide if you need to do any manual 
> parametrization. Download the .str -> .itp conversion script from the 
> MacKerell lab webpage and you're ready for GROMACS.
>
> -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/