VMD-L Mailing List

From: Goldsmith, Jacob (jgoldsmith_at_uky.edu)
Date: Tue Feb 08 2011 - 10:11:54 CST

The problem I have is this: resetpsf does not reset the topology structure. I have been trying to make multiple systems of CNTs and I have all the peices of the system in separate .pdb files. I generally write my .pdb file "by hand" with a script. Is there a way to reset the topology structure stored? Simply reloading a different topology file fails. The number of atoms in the first topology file is preserved. Thus far, I've had to exit VMD for each separate instance.

 vmd > resetpsf
clearing structure, preserving topology and aliases

What I want it to say is:
 vmd > resetpsf
clearing structure, topology, and aliases
 
Below is my construction script for reference, run in VMD 1.8.7

Thanks all,
Jacob

####################################
resetpsf
topology 12nn25c.top
# above is the topology file that changes each time
topology ru_bi_pry.top

segment BIP {
  auto angles dihedrals
  pdb ru_bi_pry.pdb
}
coordpdb ru_bi_pry.pdb

segment NT {
  auto none
  pdb 12nn25c.pdb
}
coordpdb 12nn25c.pdb NT

writepsf my_wonderful_md_trial.psf
writepdb my_wonderful_md_trial.pdb
####################################
# first few .pdb lines
ATOM 1 C000 ARM 1 8.115 -0.710 -14.757 1.00 0.00 NT C
ATOM 2 C001 ARM 1 8.115 0.710 -14.757 1.00 0.00 NT C
ATOM 3 C002 ARM 1 7.383 3.443 -14.757 1.00 0.00 NT C
ATOM 4 C003 ARM 1 6.673 4.673 -14.757 1.00 0.00 NT C
####################################
# and ... the spacing was mutilated when I c.c.p. this below
####################################
ATOM 1 RU BIPYX 1 -0.151 0.086 0.086 1.00 0.00 BIP
ATOM 2 C10 BIPYX 1 -0.051 0.708 2.913 1.00 0.00 BIP
ATOM 3 C6 BIPYX 1 -0.051 2.676 1.661 1.00 0.00 BIP
ATOM 4 C9 BIPYX 1 0.087 1.378 4.109 1.00 0.00 BIP
ATOM 5 C1 BIPYX 1 -0.221 -0.753 2.841 1.00 0.00 BIP