From: R. Charbel MAROUN (charbel.maroun_at_inserm.fr)
Date: Fri Feb 12 2016 - 05:11:39 CST
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
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