Missing coordinates and psfgen

From: Eric R Johnson (john4482_at_umn.edu)
Date: Sat Feb 07 2004 - 14:56:55 CST

I have a question about psfgen.

I am doing NAMD simulations using CHARMM parameters that contain
carbohydrates that I parameterized myself. Each one of the sugars has
many different substitution patterns. Because of this, I have a single
residue for each sugar type, but this one residue contains all possible
substituions. I will illustrate.

One of the residues is SGN which is an N-sulfate glucosamine. This
residue has the possibility of 2-O, 3-O, 6-O sulfation, or any
combination of the above. Obviously, I don't want a separate residue
for each one of these possibilities, so SGN contains definitions of all
possible atoms.

Until recently, I have been using X-PLOR to assemble the final
simulation, but would like to use psfgen. The problem is that when I
load the segment.
segment HEPA { pdb heparin.pdb }
This creates a segment with all of the possible atoms. I then load
coordpdb heparin.pdb HEPA
This sets the coordinates for all of the atoms actually contained in my
.pdb file.
At this point, in X-PLOR, I would issue the command
delete selection=( not known ) end
and it would remove all atoms without defnied coordinates.
Is this also possible in psfgen? If so, what do I need to do?
If it is not currently possible, would someone be willing to add this

Thanks so much,

  Eric R A Johnson
  University Of Minnesota                      tel: (612) 626 5115
  Dept. of Laboratory Medicine & Pathology     fax: (612) 625 1121
  7-230 BSBE                              e-mail: john4482_at_umn.edu
  312 Church Street                    web: www.eric-r-johnson.com
  Minneapolis, MN 55455    

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