From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Fri Sep 14 2007 - 11:14:36 CDT
Hi Namd users,
I am using AMBER force field to run my system and got the error message:
FATAL ERROR: The periodicity of dihedral #2 is zero.
I looked at the topology file and found out that the error message means the
parameter n equals zero for the dihedral potential k*[1+cos(n*phi+delta)] is
not acceptable. In the AMBER topology file, I have a dihedral potential like
U = C0 + C1 * [ 1 + cos(phi)]. So, I rearrange it to be U = C0/2 * [ 1 +
cos(0 * phi)] + C1 * [1 + cos(1 * phi)], then two dihedral parameter sets
are read consequently for the same dihedral. This topology file can be used
for running by AMBER, but it gave error to run in NAMD. It seems that NAMD
doesn't accept dihedral potential with zero periodicity entry. Is that true?
How to deal with it if I have to include multiple dihedral potential entries
for one dihedral with one entry has zero periodicity? Thanks a lot.
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