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

[David]

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.

> 
> Any suggestion. I am using defoult gromacs FF. Thanks in advance. Some
> my heme proteins act similar way about heme.
> 
> ...
> creating statusfile for 1 node...
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 1125 of the 1326 non-bonded parameter combinations
> WARNING 1 [file "1gal.top", line 11554]:
>   No default Bond types, using zeroes
> WARNING 2 [file "1gal.top", line 11565]:
>   No default Bond types, using zeroes
> WARNING 3 [file "1gal.top", line 11567]:
>   No default Bond types, using zeroes
> WARNING 4 [file "1gal.top", line 30699]:
>   No default Angle types, using zeroes
> WARNING 5 [file "1gal.top", line 30700]:
>   No default Angle types, using zeroes
> WARNING 6 [file "1gal.top", line 33686]:
>   No default Proper Dih. types, using zeroes
> WARNING 7 [file "1gal.top", line 33687]:
>   No default Proper Dih. types, using zeroes
> WARNING 8 [file "1gal.top", line 33689]:
>   No default Proper Dih. types, using zeroes
> WARNING 9 [file "1gal.top", line 33691]:
>   No default Proper Dih. types, using zeroes
> WARNING 10 [file "1gal.top", line 33694]:
>   No default Proper Dih. types, using zeroes
> Cleaning up temporary file grompp4Ewjbj
> Fatal error: Too many warnings, grompp terminated
>  
> 
> Best wishes
> Arturas Z.
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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