[gmx-users] No default Proper [Bond, Angle, Dihedral]

[Anton Feenstra]

David wrote:

> On Sat, 2004-01-17 at 15:20, Arturas wrote:
> 
>>Hallo,
>>
>>I got protein with prostetic group as a flavin. After grommp I've got
>>such a mess in an output (see below). Does it mean that my starting
>>structure have:
>>1. ill-defined geometry of flavin
>>2. ill-defined atom type in flavin
>>3. or it's just missing topology for flavin ??
> 
> yes, there is probably no information for flavin. the messages below
> tell you exactly where the problem is, such that you can fix it. If
> there is no information in the force field about appropriate parameters
> it is your duty to get them. if the flavin is not covalently bound you
> can use prodrg to get it.

There actually is a building block for flavin, in the (old) Gromacs FF's
as well as in the (new) Gromos ff's (43a1 etc.). I've used it and it works.
Most likely you have mismatches in atom names and/or ordering of atoms,
but normally that would have been detected and reported by pdb2gmx. Are you
useing the output .top as well as the ooutput .gro file from pdb2gmx to give
to grompp?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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