[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal (Dean Cuebas)

Dean Cuebas deancuebas at missouristate.edu
Thu Feb 19 08:00:00 CET 2009

>> Dean Cuebas wrote:
>> Dear users,
>> I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
>> I¹ve tried to get grompp to work, but I keep getting the following message:
>> _______________________________________________________
>> creating statusfile for 1 node...
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>> checking input for internal consistency...
>> calling /usr/bin/cpp...
>> processing topology...
>> Generated 165 of the 1596 non-bonded parameter combinations
>> Excluding 3 bonded neighbours for Protein             1
>> Excluding 3 bonded neighbours for IN4                 1
>> Excluding 2 bonded neighbours for SOL              8756
>> NOTE:
>>   System has non-zero total charge: 7.999998e+00
>> processing coordinates...
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.2
>> Source code file: grompp.c, line: 448
>> Fatal error:
>> number of coordinates in coordinate file (trp_b4ion.pdb, 28394)
>>              does not match topology (trp.top, 28402)
>> -------------------------------------------------------
>> It appears because grompp is ³excluding² the bonded neighbors is what¹s
>> making me end up with the different number of coordinates in my coordinate
>> and topology files.
>  No, "exclusions" are something else related to the structure of the
>  force field - atoms connected by bonds shouldn't also be modeled with
>  non-bonded interactions. The coincidence of 28402-28394=8 equaling 3+3+2
>  is just that.
>  Rather more significant is that you have a non-zero charge of (rounded)
>  8 and you seem to be part way through a process of replacing water
>  molecules with ions, which usually leaves a system neutral. I'd guess  you've
> done something wrong there - most likely mislabeled a file.
>  Mark

Thanks for your comment, I know realize the issue has nothing to do with
"exclusions but I still don't understand the problem I have.

I have the same # of molecules in the .top and the .pdf files that are going
into grompp: 1 protein, 1 ligand, and 8756 SOL. Everywhere I read, it says
that you will get a "warning" noting that the system has a nonzero charge,
before you've added any ions. That I understand, and people still generate
.tpr files to then use in genion to fix the charges.
But, why could the log say I have  8 more sets of coordinates in my .top
file than my .pdb file, which causes a fatal error, when I have identical #
of molecules????

In fact, I tested my system with the gmxtest suite 3.3.2, and got the
following simple error which also claims that a .tpr file can't be made:

No topol.tpr file in morse. grompp failed
FAILED. Check files in morse
1 out of 16 simple tests FAILED
FAILED. Check files in acetonitrilRF
FAILED. Check files in dec+water
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED

(I also reinstalled gromacs and I get the same problem)

I've followed the tutorial steps, except that I'm using version 3.3.2 on
MacOS X 10.5.6.  Any help would be so greatly appreciated.

I plan to "update that tutorial for gromacs 3.3.2" and post it back to the
gromacs site soon... IF I can get past this point.


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