[gmx-users] double-checking

[Mark Abraham]

V. Tanchuk wrote:
> Dear Users,
>     I am trying to simulate Drug – Enzyme Complex accoring to "GROMACS 
> Tutorial for Drug – Enzyme Complex" with different enzyme (ALKALINE 
> PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding water 
> with genbox I run:
>  
> grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr
> This is what I got:
>  
> creating statusfile for 1 node...
> ' for variable integrator, using 'md'
> Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
> ' for variable ns-type, using 'Grid'
> Next time use one of: 'Grid' 'Simple'
> ' for variable optimize_fft, using 'no'
> Next time use one of: 'no' 'yes'
> ' for variable constraints, using 'none'
> Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'

Your .mdp file is badly broken. Windows/Unix file type problem possibly?

> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> Excluding 3 bonded neighbours for DRG 1
> Excluding 2 bonded neighbours for SOL 21179
> Excluding 2 bonded neighbours for SOL 1711
> NOTE:
>   System has non-zero total charge: -6.999996e+00
>  
> processing coordinates...
> double-checking input for internal consistency...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 1109
>  
> Fatal error:
> There were 4 error(s) processing your input
> -------------------------------------------------------
>  
> "Working in the Burger Kings, Spitting on your Onion Rings" (Slim Shady)
>  
> 
> I would like to know what was wrong with the molecules, but there was 
> absolutely no indication of that.

Nothing as far as the above says.

> Could anyone explain what this 'double-checking' means and how to get 
> something meaningful of it?
> 
> I have also tried some Windows versions (3.2.1, 3.3). They have also 
> failed, but were able to go beyond this point. Maybe the problem is with 
> Protein_B which consists of Mg and Zn ions.

I won't rule that out, but it's not the current problem :-)

Mark