[gmx-users] methanol as a solvent

[David van der Spoel]

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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