VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 03 2013 - 10:46:47 CDT

On Wed, Jul 3, 2013 at 4:56 PM, Hunter Brown <bassoongoon_at_earthlink.net> wrote:
> Hello, I am trying to figure out how to merge pdbs, so that I can set up MD simulations with multiple molecules. When I run the mergepdbs.tcl script I get the following error:

this script has been superseded by this:

http://www.ks.uiuc.edu/Research/vmd/plugins//mergestructs/

you'll find under Extensions.

axel.

>
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 9
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 10
> psfgen) ERROR: failed on residue TYR from pdb file
> psfgen) duplicate residue key 11
> psfgen) ERROR: failed on residue GLU from pdb file
> psfgen) duplicate residue key 12
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 13
> psfgen) ERROR: failed on residue HIS from pdb file
> psfgen) duplicate residue key 14
> psfgen) ERROR: failed on residue HIS from pdb file
> psfgen) duplicate residue key 15
> psfgen) ERROR: failed on residue GLN from pdb file
> psfgen) duplicate residue key 16
> psfgen) ERROR: failed on residue LYS from pdb file
> psfgen) duplicate residue key 17
> psfgen) ERROR: failed on residue LEU from pdb file
> psfgen) duplicate residue key 18
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 19
> psfgen) ERROR: failed on residue PHE from pdb file
> psfgen) duplicate residue key 20
> psfgen) ERROR: failed on residue PHE from pdb file
> psfgen) duplicate residue key 21
> psfgen) ERROR: failed on residue ALA from pdb file
> psfgen) duplicate residue key 22
> psfgen) ERROR: failed on residue GLU from pdb file
> psfgen) duplicate residue key 23
> psfgen) ERROR: failed on residue ASP from pdb file
> psfgen) duplicate residue key 24
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 25
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 26
> psfgen) ERROR: failed on residue SER from pdb file
> psfgen) duplicate residue key 27
> psfgen) ERROR: failed on residue ASN from pdb file
> psfgen) duplicate residue key 28
> psfgen) ERROR: failed on residue LYS from pdb file
> psfgen) duplicate residue key 29
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 30
> psfgen) ERROR: failed on residue ALA from pdb file
> psfgen) duplicate residue key 31
> psfgen) ERROR: failed on residue ILE from pdb file
> psfgen) duplicate residue key 32
> psfgen) ERROR: failed on residue ILE from pdb file
> psfgen) duplicate residue key 33
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 34
> psfgen) ERROR: failed on residue LEU from pdb file
> psfgen) duplicate residue key 35
> psfgen) ERROR: failed on residue MET from pdb file
> psfgen) duplicate residue key 36
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 37
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 38
> psfgen) ERROR: failed on residue GLY from pdb file
> psfgen) duplicate residue key 39
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) duplicate residue key 40
> psfgen) ERROR: failed on residue VAL from pdb file
> psfgen) extracted 384 residues from pdb file
> psfgen) Info: generating structure...psfgen) unknown residue type HIS
> failed!
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
>
>
> What do I need to do to fix this?
>
>
> Thanks! Help is appreciated.
>
> -Hunter
>
> Hunter Brown
> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.