Re: 回复： 回复： [gmx-users] ATP/ADP+Pi

[João M. Damas]

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 <382209530 at qq.com> 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"<382209530 at 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"<gmx-users at gromacs.org>;
>
>  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"<jmdamas at itqb.unl.pt>;
>  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"<gmx-users at gromacs.org>;
>
>  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 <382209530 at 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 .
> > --
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>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613