[gmx-users] Help me!

Erik Lindahl lindahl at stanford.edu
Tue Oct 22 19:09:27 CEST 2002

pqchen at eyou.com wrote:

>Dear Erik:
>  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.



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