[gmx-users] methanol as a solvent
Nuno R. L. Ferreira
nunolf at ci.uc.pt
Wed Sep 29 16:51:17 CEST 2004
checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 3]:
Overriding atomtype OMET
WARNING 2 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 4]:
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
WARNING 3 [file "speptide.top", line 1225]:
System has non-zero total charge: -1.342595e-05
Hi Alok
These *warnings* are not errors, at least I think.
If you check the ffG41.atp file, you will find there OMET and CMET already
defined.
So, what I think its happening, is that grompp see two OMET's and two CMET's
parameters, the ones already incorporated in the gromos43a1 f.f. and in the
....WFG.itp file.
I do not know which parameters are attributed to methanol-other atoms
interactions.
I think you could rename atom types in the methanol_WFG.itp like this:
[ atomtypes ]
; type mass charge ptype c6 c12
OMET1 15.999 0.0000 A 2.26576e-3 2.325625e-6
CMET1 15.035 0.0000 A 8.87364e-3 1.936000e-5
HO 1.008 0.0000 A 0.0 0.0
[ moleculetype ]
; name nrexcl
Methanol 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CMET1 1 MeOH Me1 1 0.266000 15.035
2 OMET1 1 MeOH O2 1 -0.674000 15.999
3 HO 1 MeOH H3 1 0.408000 1.008
[ constraints ]
; ai aj funct c0
1 2 1 0.15300
2 3 1 0.10000
1 3 1 0.20770
[ exclusions ]
; ai aj ak
1 2 3
2 3 1
3 2 1
;Model "B3" from W.F. van Gunsteren et.al., JCP 112, 2000, 10450
;Christoph Freudenberger 13/03/03
;
; Edited the following atom types:
; CMET --> CMET1
; OMET --> OMET1 , Nuno R.L. Ferreira 29set04
This way I think you will not get those warnings.
About the charge warning, 10-5 is nothing. Think its roundoff errors.
Regards,
Nuno
P.S. If this protocol is wrong, please could someone shed some light on
this?
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