回复： 回复： [gmx-users] ATP/ADP+Pi

[闪耀星空]

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 .
> --
> gmx-users mailing list    gmx-users at 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-request at 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 list    gmx-users at 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-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists