[gmx-users] How to generate itp files of small moleclues for gromos96 force field

[Shulin Zhuang]

Dear All,

I use gromacs version 3.3 to perform a simulation on a protein-drug complex.
I chose the gromos96 53a6 force field. But how to generate the parameter
file of the drug fo gromos96 53a6 force field. The Dundee PRODRG server
produce files in format of gromacs/gromos87.
But the produce files of drugs such as itp file is not full agreement with
gromos96 format. For example,  in the itp file of the drug,  as far as the
bonds are  concered, in gromacs, the funct is set to 1,while in gromos96 ,it
is 2.  Should I just change the funct value to 2  to keep it in agreement
with gromos96 force field? For the atom type, I can edit them. But the bonds
parameter is difficult for me to convert them to gromos96 force field. Would
anyone give me any suggestion?

best regards

--
   Shulin Zhuang
Chemistry Department
Zhejiang University PRC
shulin.zhuang at gmail.com
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