Re: AMBER: Topology file problem in TI !

From: Pradipta Bandyopadhyay <>
Date: Thu, 8 Mar 2007 11:25:26 +0530 (IST)

Thanks, Thomas. Well, I will do electrostatic and VDW separately for my
'real system' (i.e. the protein in which I will mutate ILE to VAL). Since,
I was getting this charge problem, I am checking with only ILE (to VAL)
and plan to do electrostatic and VDW together. But the 'charge' problem
still persists. The off file has the correct charges. But since, leap is
complaining the charge of the perturbed state is non-integral, I can't
save the topology file.


> Hi Pradipta
> I'm not sure I can help you with the charge reporting problem, but here
> are some thoughts:
>> I am using AMBER 8 in a linux machine.
> Setup of TI calculations has become much easier in amber 9 (and hopefully
> will be even more so in amber10), so if you want to do lots of these
> calculations, I would seriously consider upgrading.
>> I plan to do both electrostatic and VDW in one step for this model
>> system.
>> This is what I did in xleap
> Without knowing the specifics of your system, I would advise you against
> that, reducing the vdw-repulsion on a charged atom (no matter how small
> the charge) can result in serious simulation instabilities. Doing a
> transformation in 2 steps (remove charges, then disappear the chargeless
> atoms) is annoying to set up, but needs only a little more computer time,
> because a charge-change transformation normally has a very linear
> dvdl-curve and needs only few lambda points (say, quite speculatively, 5
> compared to 20 for the vdw change).
> Considering the charge reporting problem, what I would do is make sure
> that youre .lib (or .off) files contain the right charges for all atoms,
> then you know that it is only a reporting problem in leap. While this
> advice just amounts to 'dont trust the charge command', it should not be a
> big obstacle in getting your calculation started. Someone else on the list
> might help you more here...
> Regards,
> Thomas
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 11 2007 - 06:07:13 PDT
Custom Search