AMBER: TI calculation: charge is not zero in the perturbed state

From: <>
Date: Sun, 4 Mar 2007 02:02:02 +0530 (IST)

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.

For this calculation, first I did the charging part, where I removed all the charges of the mutating atoms of the residue ILE. Secondly, for the disappearing free energy calculation we need to have changes for the Vdw parameters to zero by using the dummy atoms (DH instead of CD1 and HD instead of H-atoms attached to delta carbon CD1) and for the same I made an .frcmod file as follows.

# FRCMOD convert Isoleucine to valine.


DH   1.008

HD   1.008


DH-HD  340.0    1.090

DH-CT  310.0    1.526


CT-DH-HD    50.0      109.50

HD-DH-HD    35.0      109.50

CT-CT-DH    40.0      109.50

HC-CT-DH    50.0      109.50


HD-DH-CT-CT    1   0.16        0.0             3.

HC-CT-DH-HD    1   0.15        0.0             3.

CT-CT-CT-DH    1   0.18        0.0            -3.

CT-CT-CT-DH    1   0.25      180.0            -2.

CT-CT-CT-DH    1   0.20      180.0             1



  DH          1.9080  0.1094

  HD          1.0000  0.000

To make the .top and .crd file (for disappearing part) I loaded the .off file (which was created for the charging part) in Xleap and through Edit selected atoms made the editor table. Then I filled the charges of VAL in the unperturbed charge and the Delta charge as zero to get the final charge of VAL in the perturbed state.

The problem here is that the charge of the system is not zero in the perturbed state as complaint by Leap and is showing warning and error that “The perturbed charge:  -0.158200 is not zero and not integral”. But to my knowledge, as the delta charge is zero, the perturbed charge has to carry the charge as such in unperturbed state, which is not here what I found in my case.

Also I checked the charge of the system before loading the .frcmod file and found to be zero, but unfortunately after loading .frcmod the charge of the system is not zero (-0.158200), so I am worrying whether I have mistake in my .frcmod file or its with the mistake in my filling up the charges in the editor table. The table is attached here with, please check the charges if I would have done any mistakes.

I am using the AMBER-8 version in a Linux system.
So can anybody please point out the mistake and suggest me to overcome the problem. 

Any suggestions will be highly appreciated.

B.R. Meher









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Received on Sun Mar 04 2007 - 06:08:09 PST
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