[gmx-users] methanol as a solvent

Alok alokjain at iitk.ac.in
Thu Sep 30 11:25:40 CEST 2004

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

> 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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