AMBER Archive (2002)

Subject: Query regarding Gamess

From: Nitin Kumar Singh (nitinuec_at_iitr.ernet.in)
Date: Tue Jun 25 2002 - 10:23:09 CDT

Hello

I am trying to use Amber 6 for molecular modelling. In order to make it
widely appicable for organic molecules I am using the force fields
frovided with Amber 7 (on net). I am facing some problems in this regard.
It will be very helpful if some1 cud help me in this regard. I am
listing the steps that I have followed.

1. Making of a molecule's model on xleaps edit window.
2. Using "add H and build" command
3. saving this unit as pdb file and using gamess for charge calculation
4. Filling up the atom properties window
5. saving the unit as .lib file
6. using saveamberparm for minimization

I am using the gaff.dat file of Amber7.

However the results obtained after minimization are highly absurd. However
when I tried these steps for methane the results obtained were fairly
good. For molecules like mitoxantrone I was getting final energy of the
order of E17! However , I made a pdb file of the output using the topology
and co-ordinate files. When I tried to view it's structure using edit I am
getting a distributed array of molecules with no connectivity shown.

I would very much appreciate your help

With regards

                NITIN KUMAR SINGH
                BE(ELECTRONICS & COMMUNICATION) -III YEAR
                INDIAN INSTITUTE OF TECHNOLOGY ROORKEE, INDIA
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