AMBER Archive (2004)

Subject: AMBER: Questions about pert.charge and atom type change.

From: Chunhu Tan (
Date: Wed Jun 30 2004 - 19:20:38 CDT

 Hi, all,

    I am trying to do TI with sander, but I am still confused with the
in xleap. My question is, when a H (with the charge 0.0791) atom becomes a
dummy, if
its pert.charge is 0-0.0791=-0.0791? If this is true, why the dummy H atoms
this page have no pert.charge?
Also on this page, the first CT's charge, in VAL, is 0.2985, in ALA,
is -0.1825, so its pert.charge
should be -0.1825-0.2985=0.4810, not the 0.105, am I right?

   Another question. When I perturbed CH3-OH to CH3-SH, if both the O
atom(type OH) and the H
atom attached to it (type HO) should be changed to type SH and HS
respectively? I tried to only
change the O, but when I saveamberparmpert, LEap told me :
     No bond parameter for: SH-HO
     Can't find angle parameter: CT-SH-HO
When I also changed the H, it is OK, but I am not sure it is right, and what
about the pert.charge of H?

Thanks in advance!!

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