AMBER: Setting up thermodynamic integration

From: <>
Date: Wed, 1 Sep 2004 15:31:10 +0100

Dear list,

My question is about the perturbed bonds, angles etc. when creating a
prmtop file to be used for TI.
I am doing a fairly simple perturbation, where one -CH- group changes
to a -N-

So I use the following commands in my file:

set complex.90.C2 pertName N1
set complex.90.C2 pertType nd
set complex.90.C2 pertCharge -0.0693
set complex.90.H1 pertName LP
set complex.90.H1 pertType LP
set complex.90.H1 pertCharge -0.2255

....... (changing other charges in the residue)

saveAmberParmPert complex prmtop.uns prmcrd.uns

The prmtop.uns file produced doesn't contain any information about
perturbed bonds/angles/dihedrals
are all blank, but the PERT_ATOM_SYMBOL and PERT_CHARGE fields seem
to be fine.
The system runs apparently OK in sander with clambda = 0.5, but I'm
wondering if the blank fields should concern me. If so, how do I get
LeAP to fill them?


Dave Evans
London School of Pharmacy
The AMBER Mail Reflector
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Received on Thu Sep 02 2004 - 01:15:13 PDT
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