VMD-L Mailing List

From: Hunter Brown (bassoongoon_at_earthlink.net)
Date: Wed Jul 03 2013 - 09:56:51 CDT

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:

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