AMBER Archive (2007)

Subject: AMBER: regrading interaction energy calculations

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Sun Oct 07 2007 - 23:52:23 CDT

Hello Amber users

I am using Amber 9 , while using the anal module for calculating the
interaction energy betweeb two residues i am getting *********** at some
places instead of the energy values in the output file ,

what is the reason for that ?

I want to calculate the interaction enrgy between a particular pair of
residues but i found that it was actually calculating for all the atoms , IS
THAT TRUE?

I was getting an error sometimes "number of non bonded interactions are
more than the maximum range" but when i removed some of the atoms manually (
like if i used a coordinate file which is not having any water, in that I am
not geting the same error) even when I am using the same residue for
calculting the interaction energies in both the cases .

Energy values are given in terms of some groups in the ouput file, I think
these groups corresponds to the residues which i mention in the input file
ie 43 and 50 but if that is the case than how come there are 3 groups??? ,
it should be 2.

I am attaching my input and output files please have a look, I will be very
grateful.

Thanks & Regards

Gurpreet


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