[gmx-users] Help me!
lindahl at stanford.edu
Tue Oct 22 19:09:27 CEST 2002
pqchen at eyou.com wrote:
> I want to study a molecular used the opls force field!And my molecule is not
>a protien.How I can get the .top file.
> And how i can get the atomic charges of each atom?
> Thank in advances.
> sincerely yours
> PeiQuan Chen
Look at the descriptions in the ffoplsaa.atp file and try to build up
your molecule from smaller functional groups.
You might need a biochemistry textbook (or use google) for some of the
strange names (sorry, they are from Jorgensen, not us :-)
If there are several atom types you are hesitating between - look at the
charges and nonbonded parameters in ffoplsaanb.itp - in a lot of cases
the differences are really insignificant...
If everything works you should end up with nice and neutral molecules.
More information about the gromacs.org_gmx-users