回复： [gmx-users] About HPO4

[Justin Lemkul]

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

--
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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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