VMD-L Mailing List

From: Yasser Almeida-Hernandez (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Aug 03 2020 - 06:46:49 CDT

 

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 [1]
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
 
Links:
------
[1] https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html