VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Wed Jan 31 2007 - 14:30:11 CST

Dear John,

Thanks a lot John!
I have tried your suggestions, but things are still not working ...
Here is the summary:

1. To run example file:
....
> to load the examples as if you had started them from the command line:
> cd /your/home/directory/Desktop/1kdx
> play 1kdx.vmd

It shows up now, but the whole surface is just white. Is it something
about parameters, or something else that needs to be set up?

2. To read CHARMM el. potentila file I have upgraded to VMD 1.8.5 and
did following (two different things):

2.a) I have assumed that the proper extension for el. potential is dx
(reading examples). Is that so?

FIRST: file> new molecule> loaded CHARMM .psf file and .crd file (coordinates)
vmd > cd /Users/ivana/Desktop/UHBD/El.potential.charmm
vmd > mol addfile jws.s1.phi.0.6.watr.dx
Error reading grid dimensions.
ERROR) Could not read file jws.s1.phi.0.6.watr.dx
Unable to load file 'jws.s1.phi.0.6.watr.dx' using file type 'dx'.
vmd >

Or :

2.b)
file> new molecule> loaded CHARMM .psf file and .crd file (coordinates)
file>load state> tried to load CHARMM potential file, but it did't go
through; here is beginging on the vmd screen:

psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file /Users/ivana/Desktop/Loop
modeling/jws-prot/jws.s1.dat2.psf
Info) Analyzing structure ...
Info) Atoms: 12440
Info) Bonds: 12575
Info) Residues: 787
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
RCNE SendEventToEventTarget (suom Moved ) failed, -50
Info) Using plugin cor for coordinates from file
/Users/ivana/Desktop/Loop modeling/jws-prot/jws.s1.dat2.end.crd
Info) Finished with coordinate file /Users/ivana/Desktop/Loop
modeling/jws-prot/jws.s1.dat2.end.crd.
invalid command name
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"¢ºϓºòúºÝ$º1MºÝsºº(¾ºÓ፺jºº&ºPHºuiº7º(«º£ˇºº=º*ºøº"ºb÷º&酺ۆº¾·ºÈºo·ºЫº¾
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Thanks for your help and time,

Ivana

Thanks a lot for your time and help!

Ivana