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";
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";
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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