VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Jan 10 2004 - 17:33:36 CST

Dear Zhilei,
  Which version of VMD are you using, and on what platform? If you're
running one of the older versions of VMD on a Windows machine, that may
actually be a bug that's been fixed in the newer versions. Let me know
which specific version you're using and I should have further suggestions.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 10, 2004 at 12:18:53PM -0600, zhilei chen wrote:
> Hi,
> I used solvate command to solvate my system.
>
> Package require solvate
> solvate ER2.psf ER2.pdb -t 15 -o ER2_wb
>
>
> After solvation, I obtained the .psf and .pdb, however when I load these
> two file into vmd again, something very strange happened. If I load .psf
> first, then .pdb, I lost the protein. If I load .pdb directly, I have
> both water and protein.
>
> Here is the info I got when I load psf first:
> vmd > Info) Using plugin psf for structure file C:/ER_wb.psf
> Info) Analyzing structure ...
> Info) Atoms: 41877
> Info) Residues: 16651
> Info) Waters: 12646
> Info) Segments: 7
> Info) Fragments: 16651 Protein: 0 Nucleic: 0
> Info) Using plugin pdb for coordinates from file C:/ER2_wb.pdb
> Info) Finished with coordinates file C:/ER2_wb.pdb.
>
>
> Here is the info I got if I load pdb directly
> Info) Using plugin pdb for coordinates from file C:/ER2_wb.pdb
> Info) Using plugin pdb for structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 41877
> Info) Residues: 12869
> Info) Waters: 12624
> Info) Fragments: 12626 Protein: 1 Nucleic: 0
> Info) Finished with coordinate file C:/ER2_wb.pdb
>
> I am not sure how I losted the protein in the .psf file. Is it a bug?
>
> Zhilei 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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