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Becksteinlab / MDPOW

Calculation of water/solvent partition coefficients with Gromacs.
https://mdpow.readthedocs.io
GNU General Public License v3.0
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incompatible residue names for OPLS ions #85

Open iorga opened 7 years ago

iorga commented 7 years ago

I tried to set up a simulation using a positively charged ligand (with Gromacs 4.6) and I've got the following error.

gromacs.setup: INFO     Solvated system with tip4p.gro
gromacs.cbook: INFO     system total charge qtot = 1.0
gromacs.setup: INFO     [/lig-plus/Equilibrium/water/solvation] After solvation: total charge qtot = 1.0 = 1.0
gromacs.setup: INFO     [/lig-plus/Equilibrium/water/solvation] Adding n_cation = 0 and n_anion = 1 ions...
/sge/packs_centos/opt/python-2.7.10-CentOS6/lib/python2.7/site-packages/gromacs/core.py:551: GromacsFailureWarning: Gromacs tool failed
Command invocation: grompp -p /lig-plus/Equilibrium/water/top/system.top -c ionized.gro -maxwarn 1 -o ionized.tpr -f none.mdp
Gromacs command 'grompp' fatal error message:
GMX_FATAL  Source code file: /tmp/gromacs-4.6/src/kernel/toppush.c, line: 2316
GMX_FATAL 
GMX_FATAL  Fatal error:
GMX_FATAL  No such moleculetype CL
GMX_FATAL  For more information and tips for troubleshooting, please check the GROMACS
GMX_FATAL  website at http://www.gromacs.org/Documentation/Errors
Error code: 255

It seems that all recent versions of Gromacs (>= 4.5) have residue names in oplsaa.ff/ions.itp without the charge included (e.g. NA or BR), whereas in our ions_opls.itp that is included in the topology files these residue names contain explicitly the charge (e.g. NA+ or BR-).

I would suggest to update the residue names to make them compatible with the recent versions of Gromacs.

orbeckst commented 7 years ago

Ok, yes, ... did we really start in the 4.5 days???

orbeckst commented 7 years ago

Do you have time to fix the FF file?

orbeckst commented 3 years ago

Moved to later milestone... we survived with this bug for the last 4 years so fixing it cannot be that urgent.

iorga commented 3 years ago

@orbeckst Given that we generally use MDPOW for simulating neutral compounds, this problem should not matter. But we have never said explicitely that MDPOW handles only neutral compounds, so in the end this issue needs to be fixed at some point.

orbeckst commented 3 years ago

The way I see it, as soon as we document it, we don't have to implement it. I'd rather look at it the opposite way than you: we never promised that it would work so this issue here is an enhancement suggestion and not a bug. Maybe I can squeeze a doc edit into PR #167 .

orbeckst commented 3 years ago

But yes, we should fix the ion names.

That also means that someone needs to write a test for it etc.

We leave the issue open but it’s low priority for me. If anyone sees this as a pressing problem please comment.