From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sun Apr 08 2018 - 08:58:34 CDT
Francesco,
ParseFEP assumes constant ∆λ throughout the free-energy calculations.
Cheers,
Chris Chipot
On 4/8/18 3:46 PM, Francesco Pietra wrote:
> Hello:
> I carried out FEP for Unbound ligand in water along two segments, as
> follows:
>
> frwd-01
> 0.00 0.20 0.05 $numSteps
>
> frwd-02
> 0.20 1.00 0.10 $numSteps
>
> back-01
> 1.00 0.80 -0.05 $numSteps
>
> back-02
> 0.80 0.00 -0.10 $numSteps
>
> concatenating the results as follows:
> frwd-01.fepout > frwd.fepout
> frwd-02.fepout >> frwd.fepout
>
> back-01.fepout > back.fepout
> back-02.fepout >> back.fepout
>
> ParseFEP with SOS estimator gave error:
>
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr {$mean/$nfepdata}"
> (procedure "::ParseFEP::analysis_normal_result" line 5)
> invoked from within
> "::ParseFEP::analysis_normal_result $window $fororback $nfepdata
> $fepdata"
> (procedure "::ParseFEP::normal_parse_log" line 39)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepbofile backward "
> (procedure "namdparse" line 36)
> invoked from within
> "namdparse"
> (in namespace inscope "::ParseFEP" script line 16)
> invoked from within
> "::namespace inscope ::ParseFEP {
>
> if { [string length $::ParseFEP::fepofile] < 1 && [string
> length $::ParseFEP::fepdwfile] < 1} {
> ..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
>
>
> ParseFEP with BAR gave no error, but only partial output and no graphics.
>
> If I understand, the lambda schedule that I choose is incorrect for
> the plugin.
>
> Previously I carried out successfully the same FEP along four
> sectors, with same /\lambda throughout. Now, in view of heavy FEP with
> the complex ligand-protein, I wanted to use tight /\lambda for the
> steep regions only, apparently with a wrong protocol.
>
> Thanks for advice
>
> francesco pietra
>
>
--
Chris Chipot
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3165 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801 Phone: (217) 300-0380
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_Univ-Lorraine.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.lia-uiuc.cnrs.fr
It is hard for France to maintain a thirty-five-hour workweek when
China and India have invented a thirty-five-hour workday.
Thomas L. Friedman
_______________________________________________________________________
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