Perhaps I was not too explicit. The parameterization details are on the first supplementary information file of the first paper I sent you. Here is the direct link: http://pubs.acs.org/doi/suppl/10.1021/jp905735y/suppl_file/jp905735y_si_001.pdf
The parameters are built upon the already available ATP for 43A1, if i remember correctly. I hope this helps. Cheers, João On Sat, Oct 27, 2012 at 4:20 AM, 闪耀星空 <[email protected]> wrote: > 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"<[email protected]>; > 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"<[email protected]>; > > 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"<[email protected]>; > 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"<[email protected]>; > > 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 <[email protected]> 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 list [email protected] > > 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 [email protected]. > > * 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 list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * 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 list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
