RE: AMBER: Calculating dipole moments

From: Austin B. Yongye <>
Date: Thu, 29 Nov 2007 10:40:51 -0500 (EST)

Hi Ross,
Thanks for the response.
> Which version of AMBER are you using here?
I am using AMBER 8.

>> When I use this input:
>> Ligand_cap_coul trisaccharide
>> &cntrl
>> ntr=0,
>> nstlim=20000, nscm=2000,
>> ntx=5, irest=1, ntb=2, ntpr=100, tempi=300.0, ig=974651,
>> ntp=1, taup=1.0,
>> dt=0.0001, nrespa=1,
>> ntt=1, temp0=300.0, tautp=2.0,
>> ntc=2, ntf=2, tol=0.000001,
>> ntwr=10000, ntwx=100,
>> scnb=1.0, scee=1.0, dielc=1, cut=10.0,
>> icfe=1,
>> /
>> &dipoles
>> RES 1 4
>> END
>> END
> You do not specify clambda which I would assume you need for a TI
> calculation.

I took out the clambda and klambda inputs because I didn't think they were
required for calculating dipole moments. Does it make a difference?

> TI should not do anything to modify the charge array from which
> the permanent dipole is calculated. Hence it should not affect the dipole
> result. However, I have never tested this. Are you using the same prmtop
> file for the free energy and regular calculations?

Actually, no. I used the perturbed and regular prmtop files for the TI and
 regular calculations, respectively. As you mentioned, it is likely that
the delta charges specified in the perturbed prmtop file are the source of
the weird dipole moments. The prmtop file employed in the TI calculation
has both "CHARGE" and "PERT_CHARGE" sections. When I scale the charges in
the "CHARGE" and "PERT_CHARGE" sections, I get the charges for the
unperturbed and perturbed residues, respectively. Seems likely that the
charges employed in the dipole moment calculations are the from the
PERT_CHARGE section ie using perturbed charges for the residue I am
mutating, and unperturbed charges for the rest of the trisaccharide. In
this case, what will be the best way to proceed? Extract structures from
the TI calculation, generate a new unperturbed prmtop file, and then
compute the average dipole moment for each structure?


Austin B. Yongye
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263

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Received on Sun Dec 02 2007 - 06:07:20 PST
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