AMBER Archive (2008)

Subject: AMBER: frcmod:attn needs revision

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue Aug 12 2008 - 17:18:02 CDT

Hi
I have generated a .prep file for homocysteine and used parmchk to generate the
missing parameters. The output .frcmod is given below:
remark goes here
MASS

BOND

ANGLE
hs-sh-c1 0.000 0.000 ATTN, need revision
c1-c3-n3 67.899 109.740 Calculated with empirical approach
c1-c3-c 64.875 110.975 Calculated with empirical approach

DIHE

IMPROPER

NONBON

I want to do a MD simulation using this ligand. But i assume before that i have
to assign values to hs-sh-c1. How do i do the manual parametrization? Any help
regarding this would be highly appreciated.
Looking eagerly forward for a response.
Thanks a lot in advance.

Best regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore
India 

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