[gmx-users] NADH topology

Keserű György dr. gy.keseru at richter.hu
Fri Jun 11 10:51:25 CEST 2004

Dear Anton,

Many thanks for the help. I moved to ffG43a1 and this works fine.

Best regards,


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Anton Feenstra
Sent: Thursday, June 10, 2004 5:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NADH topology

Keserû György dr. wrote:

>>Dear gmx-users,
>>I would like to run a simulation with NADH using ffgmx. To do this I 
>>edited the corresponding pdb to match atom types listed in ffgmx.rtp 
>>and modify the residue name NADH in ffgmx.rtp to NAH. Consequently I used the residue name NAH in my pdb file. pdb2gmx successfully produced topology but grompp failed because of unknown proper torsion parameters. Would you please suggest a solution for this?
>>WARNING 1 [file "nadh.top", line 312]:
>>  No default Proper Dih. types, using zeroes

grompp tells you on which lines in the .top file to 'offending' dihedral is defined. Look up which line that is, and which atoms are part of the dihedral. Then you will have to decide which parameters you will want to use. (Why there would be a building block in the forcefield without all parameters defined, I do not know however.)

Is there a particular reason you want/need ffgmx? We discourage its use since it is quite old and much better alternatives are now available.

The most logical choice is the ffG43a1, or you may prefer OPLS instead. Most building blocks in ffgmx are also (still) present in ffG43a1...


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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