On 11/20/12 9:00 AM, 闪耀星空 wrote:
Dear Justin，
Thank you for your help！I edited a parameter about HPO4 in force field 43a1 by
myself as follows：
[ PO4 ]
[ atoms ]
P P 1.924 0
O1 OM -1.127 0
O2 OM -1.127 0
O3 OM -1.127 0
O4 OA -0.949 0
H4 H 0.404 0
[ bonds ]
P O1 gb_13
P O2 gb_13
P O3 gb_13
P O4 gb_27
H4 O4 gb_1
[ exclusions ]
; ai aj
O1 H4
O2 H4
O3 H4
[ angles ]
; ai aj ak gromos type
O1 P O2 ga_28
O1 P O3 ga_28
O1 P O4 ga_13
O2 P O3 ga_28
O2 P O4 ga_13
O3 P O4 ga_13
P O4 H4 ga_11
[ impropers ]
; ai aj ak al gromos type
[ dihedrals ]
; ai aj ak al gromos type
When I use mdrun，I found that there are some bonds O2-O3，why？And O1，O2，O3
The only bonds that exist are the ones defined in the topology. If you get some
other bizarre geometry that causes a visualization program to think there are
bonds, that rendering is not to be trusted since it is probably produced from a
simple distance search. It may also indicate errors in the topology itself
leading to these unstable configurations.
are belong to OM。How to define the dihedral？？
Use ATP as an example.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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