[gmx-users] methanol as a solvent

[David van der Spoel]

On Thu, 2004-09-30 at 11:25, Alok wrote:
> Hello Dr. david & Dr.nuno,
>                             Thanks for your suggesions.
>          As Dr.nuno suggested,i made some changes in .top file so now its
> working fine without any warning.
> Now i want to know that how can i use parameters for methanol,define in
> force field?
> If i dont change the atom name than it will take value specify in
> methanol.itp file(as i think) and if i change atom name OMET to OMET1
> and CMET to CMET1 than also it takes the value of methanol.itp.so suggest
> me if i want to take parameters define in gromax force field than         
>          what i have to do? thanks.
>                                                 Alok jain
> 
remove the atomtypes definition from the methanol.itp file.
> 
> > On Wed, 2004-09-29 at 16:51, Nuno R. L. Ferreira wrote:
> >> 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.
> >
> > That's correct.
> > So the message said that previsouly defined values for OMET and CMET are
> > replace by the new ones. Make sure which ones you want (by checking the
> > literature) and (most likely) you will want to remove the values from
> > the methanol.itp file (or the force field file if you decide otherwise).
> >
> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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