AMBER Archive (2007)

Subject: AMBER: Charges in TI calculations and leap

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Tue Jan 30 2007 - 13:35:50 CST

Dear amber users,
I am employing AMBER8 to perform TI calculations for carbohydrate ligands.
When the charge perturbation file is read by the "charge" routine in leap,
it seems that the charges are read as Qs, not as deltaQs. This leads to a
wrong output for the perturbed charges.
For example, when I perturb the charges on internal residues, and run the
"charge" command in tleap, the total unperturbed and perturbed charges are
reported as 0.0000. When I perturb charges on a terminal residue, and run
the "charge" command, the total unperturbed charge is +0.194, but the
perturbed charge is reported as 0.0000.
Thanks,
austin-
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