[gmx-users] methanol as a solvent

[Nuno R. L. Ferreira]

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?