[gmx-users] invalid order of directive moleule type

[Dallas B. Warren]

> Thanks for the valueable suggessions, but sir i am actually 
> want to use this 
> program for small molecules. I have taken  single  FAD molecule  as u 
> suggested modified the atom type as described in ffgmx.rtp, 
> program results 
> top and gro files using pdb2gmx, but while running grompp i 
> am getting the 
> error:
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# 
> checking input for internal consistency... calling 
> /usr/bin/cpp... processing topology... Generated 1284 of the 
> 1485 non-bonded parameter combinations WARNING 1 [file 
> "fad.top", line 128]:
>   No default Bond types, using zeroes
> WARNING 2 [file "fad.top", line 139]:
>   No default Bond types, using zeroes
> WARNING 3 [file "fad.top", line 141]:
>   No default Bond types, using zeroes
> WARNING 4 [file "fad.top", line 328]:
>   No default Angle types, using zeroes
> WARNING 5 [file "fad.top", line 329]:
>   No default Angle types, using zeroes
> WARNING 6 [file "fad.top", line 334]:
>   No default Proper Dih. types, using zeroes
> WARNING 7 [file "fad.top", line 336]:
>   No default Proper Dih. types, using zeroes
> WARNING 8 [file "fad.top", line 338]:
>   No default Proper Dih. types, using zeroes
> WARNING 9 [file "fad.top", line 341]:
>   No default Proper Dih. types, using zeroes
> WARNING 10 [file "fad.top", line 343]:
>   No default Proper Dih. types, using zeroes
> Cleaning up temporary file gromppLLm3l8
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: fatal.c, line: 416
> Fatal error:
> Too many warnings, grompp terminated
> -------------------------------------------------------
> "I Need Love, Not Games" (Iggy Pop & Kate Pierson)

Those errors mean exactly what they say, you have no definition (in the
forcefield that you have used) for those bonds, angle and proper
dihedral types.

> Moreover , suppose if we want to use this program (grompp) for say, a 
> molecule which has no entry in any .rtp file provided with 
> Gromacs and we 

grompp doesn't use the .rtp files, that is for pdb2gmx.

> use the PRODRG server, then how to deal with the error 
> "invalid  molecular 
> directive type".

Amazing what you can find by searching the emailing list ;)

http://www.gromacs.org/external/search.html

http://www.gromacs.org/pipermail/gmx-users/2006-November/024540.html

http://www.gromacs.org/pipermail/gmx-users/2003-December/008346.html

Might be an idea to have a read through the manual as well, particularly
the chapters on topologies.