VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Apr 24 2009 - 01:41:07 CDT

Next message: accomp lin: "Re: installed plugin won't show up next time"
Previous message: Leandro Martínez: "Re: local packing density around a chemical group (say, a methyl group or a side chain)"
Next in thread: John Stone: "Re: Error processing bonds"
Reply: John Stone: "Re: Error processing bonds"
Reply: Axel Kohlmeyer: "Re: Error processing bonds"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I am trying to solvate a protein using the solvate plugin of VMD. The PSF
(X-PLOR format) and PDB were produced with CHARMM. I get the following
error:

vmd > solvate protein_xplor.psf protein.pdb -minmax {{-65 -65 -65} {65 65 65}}
reading structure from psf file protein_xplor.psf
Error processing bonds

I'm using vmd version 1.8.6 on linux.

I have uploaded the files here:

http://artemide.bioeng.washington.edu/Files/protein_xplor.psf

http://artemide.bioeng.washington.edu/Files/protein.pdb

Any help would be appreciated.

Gianluca