回复： [gmx-users] About HPO4

[闪耀星空]

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 are belong to OM。How to define the dihedral？？

 

 

xiaohong

 

------------------ 原始邮件 ------------------

发件人: "Justin Lemkul"<jalem...@vt.edu>;

发送时间: 2012年11月20日(星期二) 晚上8:30

收件人: "Discussion list for GROMACS users"<gmx-users@gromacs.org>;

主题: Re: [gmx-users] About HPO4

On 11/20/12 4:03 AM, 闪耀星空 wrote:
> Hi,
>   HPO4 has dihedral or  not??    If it has,which one?
>
>

There likely is a dihedral you need to use (since there are 4 atoms in O-P-O-H),
but the second answer depends on which force field you are using.  Without
knowing that, no one can say.

-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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