[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal (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
>> 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.
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 #
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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