AMBER Archive (2004)

Subject: Re: AMBER: FEP error/early termination - why?

From: Sébastien Osborne (sosborne_at_science.uottawa.ca)
Date: Mon May 31 2004 - 13:12:54 CDT

sorry for confusion... different person... different simulation... I am
doing asn --> asp and the other persone was doing another.

Carlos Simmerling wrote:

> you originally said you tried asp-->ala, that is why dac mentioned
> decoupling.
> now you say you are doing asn-->asp. which is right?
> also, since you are removing a formal charge, it is not at
> all surprising that your free energy curve differs from val-->ala
> where the only change is really size.
> carlos
>
> ----- Original Message -----
> From: Sébastien Osborne <mailto:sosborne_at_science.uottawa.ca>
> To: amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> Sent: Monday, May 31, 2004 1:51 PM
> Subject: Re: AMBER: FEP error/early termination - why?
>
> what exactly do you mean by "decoupling the charge change and the
> VDW change"? I am trying to do the following perturbation: ASN
> --> ASP where the NH2 part of ASN becomes O. In the process, I am
> perturbing the hydrogen atoms to dummy atoms. Are you saying it
> is better to perform 2 runs, a first run where the hydrogen
> becomes "charged" dummy atoms (no change on the charge in the run)
> followed by a second run where the charge on the dummy atoms become 0?
>
> Thanks for the help.
>
> Sebastien Osborne
> University of Ottawa
>
> David A. Case wrote:
>
>>On Mon, May 31, 2004, Annette Höglund wrote:
>>
>>
>>>I have tried to run an initial free energy perturbation for a ASP->ALA
>>>sidechain in a protein-DNA complex (after minimization and
>>>equilibration) using a similar gibbs input as in the val-to-ala tutorial.
>>>For this particular sidechain the FEP terminates after about 75% with
>>>the arror message: "ERROR TERMINATION DUE TO SHAKE OR TORCON"
>>>When I plot the F_energy it seems to be a "concave" rather than "convex"
>>>curve (as in the tutorial).
>>>
>>>
>>
>>Are you decoupling the charge change from the van der Waals change? (Not
>>doing that _could_ lead the symptom you cite, but that is just a guess.) Be
>>sure to run the ASP->ALA change in water first (since it is simpler, and can
>>help you debug your scripts), before trying it in the protein/DNA system.
>>
>>...good luck...dac
>>
>>
>>

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