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 ScientistDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: 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 P1.924 0
O1OM   -1.127 0
O2OM   -1.127 0
O3OM   -1.127 0
O4OA   -0.949 0
H4H 0.404 0
  [ bonds ]
 PO1gb_13
 PO2gb_13
 PO3gb_13
 PO4gb_27
 H4   O4gb_1
   [ exclusions ]
;  aiaj
O1H4
O2H4
O3H4
  [ angles ]
;   aiajak  gromos type
O1 PO2ga_28
O1 PO3ga_28
O1 PO4ga_13
O2 PO3ga_28
O2 PO4ga_13
O3 PO4ga_13
P  O4   H4ga_11
  [ impropers ]
;  aiajakal   gromos type
  [ dihedrals ]
;  aiajakal   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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