From: Axel Kohlmeyer (
Date: Thu Nov 15 2007 - 03:33:31 CST

On Thu, 15 Nov 2007, Francesco Pietra wrote:

FP> axel:
FP> Yes, my posting was badly organized.
FP> combine.tcl is from

FP> I do not attach it here because my subsequent managing has shown that the
FP> problem is with protein.psf file. This is the result of not sticking to a

i am inclined to disagree. please check the log file and you'll
see, that apart from some warnings, the major complaint and error
message is that the script cannot find the .pdb file protein_aligned.pdb
that is the correctly oriented and aligned version of protein.pdb.

the rest are warnings and for as long as you were using the same
topology file to build those .psf files, i would assume, that they
are still usable.

FP> single house. I use Amber9 for MD, DOCK6.1 for docking, Chimera for
FP> dockprep, and VMD for what that world is unable to do, or simply to
FP> have a better insight. That mixture would require a better general
FP> command than I have presently attained.

this needs no comment.


FP> Looking at protein_autopsf_tmpfile.pdb with Chimera, it is clear that the
FP> procedure has removed the three "TER" records that I had set to get rid of
FP> three 50A-long bonds (those long bonds are not revealed by VMD - at least not
FP> in my default use of it - though they hinder dockprep workind and, in any case,
FP> create problems to MD).

that (again) is a reasoning, that does not make much sense to me.
the bonding information should be read from the .psf file. unless
there are CONECT records, there is no bonding information in a .pdb
file and what a program makes out of that is due to the logic (or
lack thereof) of that program.


FP> Thanks
FP> francesco

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.