From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Feb 12 2016 - 11:04:28 CST
1.) VMD doesn't register commands executed from plugins as far as I can
tell. PBC commands are technically a plugin, not an internal command, so
they aren't registered.
2.) Instead of waitfor 1, try waitfor -1. What is happening is that
there are only 6 or 8 frames loaded when the next command executes,
since the load command unhelpfully return control to the interpreter
after loading 1 frame (that is what waitfor 1 does). You want -1, which
basically tells the interpreter to proceed only after *ALL* frames are
loaded.
-Josh Vermaas
PS, this is very much a VMD question, which has a separate listserv. :)
On 02/12/2016 05:11 AM, R. Charbel MAROUN wrote:
> Hello to all,
>
> So that I can execute later on a command file, I activate "Log tcl
> commands to a file", then read an MD trajectory, do an unwrapping on a
> protein and then on its ligand, either on the tcl/tk console or in the
> vmd command line, save the new trajectory and "Turn off logging".
>
> First problem, the unwrap commands do not get registered in the file :
>
> # VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> # Log file
> '/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test_traj7.vmd',
> created by user cmaroun
> menu files off
> menu files on
> display resetview
> mol new
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/step762_prod.dcd}
> type {dcd} first 0 last -1 step 100 waitfor 1
> animate style Loop
> mol addrep 0
> display resetview
> mol addfile
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/C_3CAP-H2ODow-HME_sol_ion.psf}
> type {psf} first 0 last -1 step 100 waitfor 1 0
> animate style Loop
> animate goto 149
> animate goto 149
> menu save off
> menu save on
> animate write dcd
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test14.dcd}
> beg 0 end 149 skip 1 0
> # VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> # end of log file.
>
>
> So, I find out that I should insert them just before each "animate"
> line. The new command file is :
>
> # VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> # Log file
> '/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test_traj7.vmd',
> created by user cmaroun
> menu files off
> menu files on
> display resetview
> mol new
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/step762_prod.dcd}
> type {dcd} first 0 last -1 step 100 waitfor 1
> animate style Loop
> mol addrep 0
> display resetview
> mol addfile
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/C_3CAP-H2ODow-HME_sol_ion.psf}
> type {psf} first 0 last -1 step 100 waitfor 1 0
> animate style Loop
> pbc unwrap -sel protein
> animate goto 149
> pbc unwrap -sel "resname HME"
> animate goto 149
> menu save off
> menu save on
> animate write dcd
> {/data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test14.dcd}
> beg 0 end 149 skip 1 0
> # VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> # end of log file.
>
>
> When I submit the file to vmd :
>
> vmd -e test.vmd
>
> the second problem comes in : VMD starts reading the I/P trajectory,
> but before it finishes, it starts executing the two unwrappings, so
> that it unwraps the protein for 6 frames only and then the ligand
> (HME) for only 8 frames. Obviously, it gives an ERROR and writes down
> an incomplete trajectory :
>
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Info) Using plugin dcd for coordinates from file
> /data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/step762_prod.dcd
> 0
> psfplugin) Detected a Charmm PSF file
> Info) Using plugin psf for structure file
> /data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/C_3CAP-H2ODow-HME_sol_ion.psf
> Info) Analyzing structure ...
> Info) Atoms: 110126
> Info) Bonds: 93069
> Info) Angles: 103010 Dihedrals: 79075 Impropers: 1149
> Cross-terms: 319
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 27446
> Info) Waters: 26861
> Info) Segments: 23
> Info) Fragments: 27126 Protein: 1 Nucleic: 0
> 0
> Info) 28.6% complete (frame 1)
> Info) 100.0% complete (frame 6)
> Info) 22.2% complete (frame 1)
> Info) 100.0% complete (frame 8)
> ERROR) Illegal frames requested for coordinate file I/O
> Info) Opened coordinate file
> /data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test14.dcd
> for writing.
> Info) Finished with coordinate file
> /data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/test14.dcd.
> 0
> vmd > Info) Coordinate I/O rate 47.1 frames/sec, 59 MB/sec, 3.2 sec
> Info) Finished with coordinate file
> /data/montclient/lmoreno/pc3/3aEtapa_Produccion/Prod_3CAP_RotW100_Modif/sercal_rest/step762_prod.dcd.
>
>
> I tried "Load visualization state". Same results.
>
> Does anybody know:
> 1) Why some commands don't get registered in the command file ?
> 2) What command(s) to use to ask VMD to wait for the first command to
> finish (upload trajectory) before executing the second command
> (unwrap) and then the third (download trajectory) ?
>
> Greetings and thanx for any help. CM
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:10 CST