VMD-L Mailing List
From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Aug 03 2020 - 09:28:00 CDT
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Can you try using one of the latest 1.9.4 alpha builds and see if the problem still occurs?
Best,
JC
> On Aug 3, 2020, at 7:46 AM, Yasser Almeida-Hernandez <yasser.almeida-hernandez_at_uni-due.de> wrote:
>
> Hello,
>
> I am optimizing 2 angles in a molecule (VMD for LINUXAMD64, version 1.9.3). After filling all fields and hit 'Run optimization' nothing happens. I generated the TCL script, and when executed, it runs apparently OK but the end of the BondedOpt.debug.log ends with:
>
> NAMD run complete
>
>
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
> DONE
> downhill: optimization -downhill -tol 0.001 -iter 500 -function ::ForceFieldToolKit::BondAngleOpt::optBondsAngles
>
> Raw Result: {45 109 45 109} 0.0
>
> DONE
>
> The BondedOpt.log is:
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
>
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
>
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
>
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
>
> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>
>
> FINAL PARAMETERS
> angle {CG2O5 CG321 OG301} 45.0000 109.0000
> angle {CG2O5 CG321 OG303} 45.0000 109.0000
> END
>
> ... so no angle is optimized, since those are the initial values. I set those as initial and repeated but got the ame result.
>
> Also in the VMD terminal it states:
> ERROR) Invalid last frame: 1
> Info) Using plugin namdbin for coordinates from file min-bondangles.coor
> Info) Finished with coordinate file min-bondangles.coor.
> Info) Opened coordinate file namd-temp.pdb for writing.
> Info) Finished with coordinate file namd-temp.pdb.
> Info) Opened coordinate file namd-temp.dcd for writing.
> Info) Finished with coordinate file namd-temp.dcd.
> ERROR) Invalid last frame: 1
> Info) Using plugin namdbin for coordinates from file min-bondangles.coor
> Info) Finished with coordinate file min-bondangles.coor.
> Info) Opened coordinate file namd-temp.pdb for writing.
> Info) Finished with coordinate file namd-temp.pdb.
> Info) Opened coordinate file namd-temp.dcd for writing.
> Info) Finished with coordinate file namd-temp.dcd.
> ERROR) Invalid last frame: 1
> Info) Using plugin namdbin for coordinates from file min-bondangles.coor
> Info) Finished with coordinate file min-bondangles.coor.
> Info) Opened coordinate file namd-temp.pdb for writing.
> Info) Finished with coordinate file namd-temp.pdb.
> Info) Opened coordinate file namd-temp.dcd for writing.
> Info) Finished with coordinate file namd-temp.dcd.
> ERROR) Invalid last frame: 1
> Info) Using plugin namdbin for coordinates from file min-bondangles.coor
> Info) Finished with coordinate file min-bondangles.coor.
> Info) Opened coordinate file namd-temp.pdb for writing.
> Info) Finished with coordinate file namd-temp.pdb.
> Info) Opened coordinate file namd-temp.dcd for writing.
> Info) Finished with coordinate file namd-temp.dcd.
> ERROR) Invalid last frame: 1
>
> What ERROR) Invalid last frame: 1 means? I read the thread https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html <https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html> but was not very helpful.
>
> Any help or advice with this issue will be very much appreciated since I have been stuck with this since a while.
>
> Best,
> Yasser
>
> --
> Dr. Yasser Almeida-Hernandez
> Postdoctoral Researcher
> Computational Biochemistry
> T03 R01 D45
> Faculty of Biology
> University of Duisburg-Essen
> Universitätsstr. 2, 45117 Essen
> Email: yasser.almeida-hernandez_at_uni-due.de
> Phone: +49 201 183 2457
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