[gmx-users] grompp error! why?

[Erik Marklund]

You include unk.itp but show us drg.itp. Perhaps you're looking at or 
using the wrong file.

/Erik

qing yang skrev:
>
> Dear gmx-users,
>
> I am try to simulate the protein-drug, and have used drg.itp from 
> prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs. 
> But when I issue a grompp command for minimization,grompp gives a 
> fatal error.
>
> The error is:
>
> Error 0 [file "unk.itp",line 4]
>
> Not enough parameters
>
> …..
>
> Fatal error:
>
> Bonded/nonbonded atom type '1' not found!
>
> My pro.top file:
>
> #include “ffg43a1.itp”
>
> #include “unk.itp”
>
> [molecules]
>
> Protein 1
>
> UNK 1
>
> SOL 109324
>
> My drg.itp file:
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CR1 1 UNK CBF 1 0.003 12.0110
> 2 HC 1 UNK HBF 1 0.035 1.0080
> ...............
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 0.109 12300000.0 0.109 12300000.0 ; CBF HBF
> 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG
> .............
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 6 1 ; CBF NBK
> 1 9 1 ; CBF CBI
> .................
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 2 1 3 2 120.0 505.0 120.0 505.0 ; HBF CBF CBG
> 2 1 13 2 120.0 505.0 120.0 505.0 ; HBF CBF CBE
> ................
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp CBF CBE CBG HBF
> 3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBG
>
> Maybe someone knows what the problem might be?How can I deal with this 
> problem?
> Thanks for your help!


-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys