From: Shirley Li (li19104_at_yahoo.com)
Date: Thu Dec 22 2005 - 16:54:06 CST
Thank you so much for your very helpful information and detailed instruction. After the following changes as you suggested:
BOND OH2 H1 OH2 H2 H1 H2 ==> BOND OH2 H1 OH2 H2
C2' CN7 in ATP ===> C2' CN7B
C5' CN8 in ATP ===> C5' CN8B
Now the minimization works fine.
Many thanks again for your kind help.
Peter Freddolino <petefred_at_ks.uiuc.edu> wrote: Hi Shirley,
just for the list's sake, I'll point out to everyone that the problem
with the CN7 atoms that Shirley originally posted is just because the
angle consisting of 3 CN7 angles is not in the standard parameter file;
it doesn't matter if you've used CN7 atoms before because each angle is
The issue with the HT HT OT angle that you're experiencing means that
the waters that you have contain an extra bond between the two
hydrogens. This is present in some topology files and is a legacy of
SHAKE and charmm, which needed this bond to accurately maintain the
planarity of water molecules. This bond is not needed anymore for NAMD,
and I generally advise people to remove it. How did you generate your
psf file? The easiest way to do this is usually to modify your topology
file and then regenerate your psf. This is done by changing the RESI
TIP3 entry in your topology file to read
RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
PATCHING FIRS NONE LAST NONE
(This is the form now found in the namd tutorial).
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