From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Aug 31 2006 - 15:24:36 CDT
Hi again,
First, the warning from Marcos applies to all of the c31b1 and c32b1
topology files, not just those with CMAP terms. (These are available at
http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm)
Second, if you have any waters in your system with the standard CHARMM
"third bond" between the hydrogens, when you regenerate angles and
dihedrals you'll end up with two extra angles per water. Since these have
no parameters it's "safe" in the sense that NAMD will report an error.
The solution is to remove the third bond from the TIP3 definition in the
topology file since NAMD doesn't need it.
Third, the HSP residue is missing its CMAP term. It can be easily copied
from, e.g., HSD.
-Jim
On Thu, 31 Aug 2006, Marcos Sotomayor wrote:
>
> 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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