AMBER Archive (2006)

Subject: AMBER: TI-FEP for ILE--->VAL.

From: Biswa Ranjan Meher (brmeher_at_iitg.ernet.in)
Date: Thu Aug 03 2006 - 00:26:22 CDT

Dear AMBER users,

For our protein-drug system: we are doing the free energy perturbations in
a transformation of ILE --->VAL using the TI method. We are using dummy
atoms for the missing group -CH2 while transforming from ILE --> VAL.

  So in order to make the .frcmod file for the dummy atoms we need to
have changes for the charges and Vdw parameters to zero.

Regarding the force constants for bond, angle and dihedral parameters
involving the dummy atoms - should it be same as in ILE?

Since the bond, angle parameters and dihedral barriers are artificial for
dummy atoms I am worrying if that can affect the free energy difference.

Or should I put smaller values for those parameters just to keep the
dummy atoms in place.

I would appreciate your suggestion.

Regards
B.R. Meher 

-- 
......................XXXXXXXXXXXXXXXXXX................................
Mr. Biswa ranjan Meher (Research Scholar)          Room:119
Dept. Of Biotechnology, IIT-Guwahati,              Siang Hostel
North Guwahati, Assam-781039                       IIT-Guwahati
Phone:0361-2582246(Lab)                            Phone:0361-2582766/7/8
...........................................
Mob:+919435014189
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