[gmx-users] RE: simulation of a metal binding sites

2011-02-17 Thread Ran Friedman
the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph

Re: [gmx-users] RE: simulation of a metal binding sites

2011-02-17 Thread bharat gupta
. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph

Re: [gmx-users] RE: simulation of a metal binding sites

2011-02-17 Thread Justin A. Lemkul
...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com mailto:aanlktin06ut6%2bwrfpz4a79fq9g

Re: [gmx-users] RE: simulation of a metal binding sites

2011-02-17 Thread Marc Baaden
Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental

Re: [gmx-users] RE: simulation of a metal binding sites

2011-02-17 Thread bharat gupta
Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other

[gmx-users] RE: simulation of a metal binding sites

2011-02-16 Thread bharat gupta
Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No.