[gmx-users] Choosing a f.f. biopolymer system & WFG B3 methanol model

[Nuno R. L. Ferreira]

Hello

A simple one.
My aim is to do some MD sim's with a system composed of protein and solvent
(+ ions if necessary) and eventually sooner or later, micelles and bilayers.
Searching the gmx e-mail list, got the opinion that the "best" forcefield to
use with this kind of systems is the gromos96 43a2x. Is that right?

Another one.
In the GROMACS f.f. topologies (molecules) homepage, there's the B3
three-site methanol model (parameters proposed by van Gunsteren) posted by
Christoph Freudenberger. Can I use it under gmx and gromos forcefields just
like that? Nothing to be changed in the function values (constraints field)?
I prepared a system with a peptide and this B3 model.  grompp says that is
overiding OMET and CMET atomtypes . Because the same atomtypes exist in the
ff...rtp file, right?
For a quick inspection, here's the B3 model:

[ atomtypes ]
;   type      mass    charge    ptype              c6                 c12
    OMET    15.999     0.0000     A     2.26576e-3      2.325625e-6
    CMET    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       CMET     1       MeOH    Me1     1        0.266000  15.035
2       OMET     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

By the way. I'm enjoying working with this super program. I'm getting
disapointed never have had the chance to learn C. Think gonna start.

Regards,
Nuno



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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
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