From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Aug 31 2006 - 11:04:03 CDT
Dear all,
The latest CHARMM topology files (toppar_c32b1.tar), which
include the cmap correction, do not include angle/dihedral information
for several (if not all) patches. This means that whenever you are
building your structures with psfgen in VMD, a patch statement outside the
generate statement NEEDS TO BE FOLLOWED BY the psfgen command "regenerate
angle dihedrals" (see example below).
Marcos.
BEFORE:
package require psfgen
topology toppar/top_all27_prot_lipid.inp
...
segment A { pdb lyso.pdb}
patch DISU A:6 A:127
coordpdb lyso.pdb A
...
NOW:
package require psfgen
topology toppar/top_all22_prot_cmap.inp
...
segment A { pdb lyso.pdb}
patch DISU A:6 A:127
coordpdb lyso.pdb A
regenerate angles dihedrals
...
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