VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Jan 30 2008 - 15:06:49 CST

I'm having trouble visualizing how to use MDenergy to post-process a dcd file, probably because I have a glycan ligand & had to use amber-style input. (2 of the glycans have types over & above the CSFF pyranosides).

Here's my wrapper script, which I input into VMD in command line mode, batch processing because my trajectory is so large:

 source /nas0/einew/mdenergy.tcl
 mol load parm7 trla.prmtop dcd trla1.dcd
 set sel1 [atomselect top "resid 1444 to 1449"]
 set sel2 [atomselect top "protein"]
 mdenergy -elec -sel $sel1 $sel2 -ofile "h5eleca.dat" -beg 0 -end last \
-switch 11 -cutoff 13 -amber trla.prmtop -dcd h5lall.dcd

trla1.dcd is the first frame of h5lall.dcd. I did that because if I loaded the entire dcd
file here to make the selections, I'm defeating mdenergy's memory-saving frame-at-a-time operation.

But I get this error message:

Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 3879MB (96%)
Info) Using plugin parm7 for structure file trla.prmtop
Info) Analyzing structure ...
Info) Atoms: 134546
Info) Bonds: 134745
Info) Residues: 38761
Info) Waters: 37202
Info) Segments: 1
Info) Fragments: 37309 Protein: 6 Nucleic: 0
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 trla1.dcd
Info) Finished with coordinate file trla1.dcd.
0
atomselect0
atomselect1
0
can't read "stype="parm7"": no such variable
Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

Which indicates there's some sort of incompatibility. How do I do this correctly?

Thanks!
Irene Newhouse
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