AMBER Archive (2008)

Subject: Re: AMBER: Can sander provide ESP with PBC?

From: John Chodera (
Date: Mon Apr 21 2008 - 21:24:25 CDT

Hi Khatcharin,

I think I am trying to do something similar to what you describe. I
don't believe AMBER can currently compute the electrostatic potential
on specified atoms by manipulating input flags, but it obviously does
compute the potential as part of the energy computation during normal

Specifically, I am trying to modify a version of AMBER10's sander
module to also write out the electrostatic potential and its first and
second derivatives (which includes information on the electric field
and its gradient) at specified atoms when running with a fixed-charge
forcefield using PME. We're interested in using this to compute
spectroscopic observables like FTIR spectra, but you may find this
useful for your own purposes as well.

Does this sound like it would be helpful to you? I can let you know
when we have something working (hopefully in the next few days), and
then can give you a patchset to try. We couldn't really support it,
but it might at least help you get started.


- John

Dr. John D. Chodera <>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021

On 21/04/2008, Khatcharin Siriwong <> wrote: > > > Dear All, > > I am using amber9 and I have an MD trajectory generated by sander module. I > would like to calculate the energy of the system in each snapshot for some > resons. Is it posiple that sander (or another module) can provide the > electrostatic potential (ESP) on atoms by taking into account the periodic > boundary condition? If yes, what keyword should be used and do I need to > re-generate the trajectory? > > Thank you very much in advance. > > Regards, > > Khatcharin > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector To post, send mail to To > unsubscribe, send "unsubscribe amber" to ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to