VMD-L Mailing List

From: zhilei chen (zchen4_at_uiuc.edu)
Date: Sat Jan 10 2004 - 12:18:53 CST

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