回复： [gmx-users] About HPO4
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 -- gmx-users mailing listgmx-users@gromacs.org http://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
[gmx-users] About HPO4
Hi, HPO4 has dihedral or not?? If it has,which one?-- gmx-users mailing listgmx-users@gromacs.org http://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
回复： 回复： [gmx-users] ATP/ADP+Pi
Hello How to parameterize ATP, ADP and Pi ?my initiating structure has it,but the force field has not define the ATP,ADP,Pi and not recognition it .thanks -- 原始邮件 -- 发件人: "闪耀星空"<382209...@qq.com>; 发送时间: 2012年10月27日(星期六) 中午11:03 收件人: "Discussion list for GROMACS users"; 主题: 回复： [gmx-users] ATP/ADP+Pi Thanks for your help!! About these paper,I have just read them. In your paper,you selected 43a1 force field directly and did not talk about ATP/ADP+Pi parameters.But in my 43a1 force field ,the ATP parameters are exist,ADP and Pi are not.I use gromacs 4.5.5 versions. WHY?? Thanks!! -- 原始邮件 -- 发件人: "João M. Dama"; 发送时间: 2012年10月26日(星期五) 晚上11:38 收件人: "Discussion list for GROMACS users"; 主题: Re: [gmx-users] ATP/ADP+Pi Hello, At our group we have parameterized ATP, ADP and Pi to use with ABC transporters. Paper with the parameterization: http://dx.doi.org/10.1021/jp905735y Papers using the parameterized molecules: http://dx.doi.org/10.1002/prot.23023 http://dx.doi.org/10.1002/pro.650 http://dx.doi.org/10.1371/journal.pcbi.1002128 Cheers, João On Fri, Oct 26, 2012 at 4:12 PM, 闪耀星空 <382209...@qq.com> wrote: > GMX-users: >I am working with ATP+protein and ADP+Pi+protein in gromos43a1.ff > force field,but I find only ATP parameters in the aminoacids.rtp file > .Where can I achieve the ADP+Pi parameters ??? I wanted use the > parameters from((http://www.pharmacy.manchester.ac.uk/bryce/amber) ) > but it seemed unsuitable . What can I do??? Please help me with this. > > Thank you very much . > -- > gmx-users mailing listgmx-users@gromacs.org > http://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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http://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-- gmx-users mailing listgmx-users@gromacs.org http://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
回复： [gmx-users] ATP/ADP+Pi
Thanks for your help!! About these paper,I have just read them. In your paper,you selected 43a1 force field directly and did not talk about ATP/ADP+Pi parameters.But in my 43a1 force field ,the ATP parameters are exist,ADP and Pi are not.I use gromacs 4.5.5 versions. WHY?? Thanks!! -- 原始邮件 -- 发件人: "João M. Dama"; 发送时间: 2012年10月26日(星期五) 晚上11:38 收件人: "Discussion list for GROMACS users"; 主题: Re: [gmx-users] ATP/ADP+Pi Hello, At our group we have parameterized ATP, ADP and Pi to use with ABC transporters. Paper with the parameterization: http://dx.doi.org/10.1021/jp905735y Papers using the parameterized molecules: http://dx.doi.org/10.1002/prot.23023 http://dx.doi.org/10.1002/pro.650 http://dx.doi.org/10.1371/journal.pcbi.1002128 Cheers, João On Fri, Oct 26, 2012 at 4:12 PM, 闪耀星空 <382209...@qq.com> wrote: > GMX-users: >I am working with ATP+protein and ADP+Pi+protein in gromos43a1.ff > force field,but I find only ATP parameters in the aminoacids.rtp file > .Where can I achieve the ADP+Pi parameters ??? I wanted use the > parameters from((http://www.pharmacy.manchester.ac.uk/bryce/amber) ) > but it seemed unsuitable . What can I do??? Please help me with this. > > Thank you very much . > -- > gmx-users mailing listgmx-users@gromacs.org > http://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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http://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-- gmx-users mailing listgmx-users@gromacs.org http://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
