[gmx-users] double-checking

[V. Tanchuk]

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'

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. 

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.


Thank you in advance for your help.
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