VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Thu Feb 01 2007 - 08:28:20 CST

(I have send this e-mail yesterday, but since it still didn't show up
on VMD list I am resending it)

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. potential 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 beginning 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
",??????Ñ????????????s???????????????????????????????,??????0??????????????????T@???????????????????????????????????????????????????????????ð?0??????ÜPæ??_¡xºj>zº
Ý{º¸~}ºQ!ºnbºà4ºÕºâڂº÷ º"
invalid command name "ùºÂʇººFkºÓ9º??ºҋº·ºdº§*º=w¯ºômº´)ºS⑺µºIºý÷º뢔ºIº"
invalid command name
"ºAºxº֮ºÂ䃺zzº58|ºýâ}ºººÀvºOº(ºuº»ڄºM´º{ºÄfºC??º¸º/ގºQªºþsº]"
invalid command name "ºº£ºg'º(r)¥ºâº(ºrüºGb
ºç`ºJº2n¡ºdº¡º????¢ºç>¢ºw¢º¨¢ºâҢºÐö¢º£º )£º28£ºW@£º)A£º%"
invalid command name "tºLZº¡@º]'ºôºڊºñ¿º¤ºpº2kº?LºÓ+ºÉ"
invalid command name "㤺??¥º#¥ºÖ8¥ºÑF¥ºM¥º6M¥ºE¥º¨6¥ºM"
invalid command name "¥º ¤ºàF¤ºÇ٣ºcf£ºê좺m¢ºÏ硺Ç¡º̠º'6 ºùºòúºFVºý¬º%ޚºó"
invalid command name "ºAºrº"
invalid command name
"¢ºϓºòúºÝ$º1MºÝsºº(¾ºÓ፺jºº&ºPHºuiº7º(«º£ˇºº=º*ºøº"ºb÷º&酺ۆº¾·ºÈºo·ºЫº¾
º°ºóº×}ºqº~cºTºZDºc2ºººkðº}Ֆºݷº̖º¸rºâJº0ºk»º"
invalid command name "º"

I could upload my .psf, crd and potential files if yopu would like to
check them out ...

Thanks for your help and time,

Ivana