From: Fulu Zheng (flzheng525_at_gmail.com)
Date: Sat Jul 05 2014 - 02:05:28 CDT
Dear All,
I add a CTER to the LYS residue, but the distance between two O atoms in
the CTER group becomes unusually small (0.271 angstrom) during the MD
simulation.
The CTER group used in my simulation is as follows:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PRES CTER -1.00 ! standard C-terminus
GROUP ! use in generate statement
ATOM C CC 0.34 ! OT2(-)
ATOM OT1 OC -0.67 ! /
ATOM OT2 OC -0.67 ! -C
DELETE ATOM O ! \\
BOND C OT2 ! OT1
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
The parameters for OC in VDW is as follows:
OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
! JG 8/27/89
Any idea about this problem?
Thank you so much!
Fulu
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