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 .
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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