[gmx-users] binding sites with MD

[Michael Shirts]

Vmd can convert trajectories, as can other tools. Google is your friend!

Sent from my iPhone

> On May 24, 2014, at 15:13, Albert <mailmd2011 at gmail.com> wrote:
> 
> this plug-in looks interesting.
> 
> However, as far as I saw from the tutorial that even we run simulation from Gromacs, this plugin can only import NAMD psf and DCD to analysis. That's  a headache issue. Can you improve this vmd plugin so that it can also read Gromacs format files directly?
> 
> best
> Albert
> 
> 
>> On 05/24/2014 07:02 PM, Tom Dodson wrote:
>> Nidhi,
>> 
>> You might be interested in this tool:http://prody.csb.pitt.edu/drugui/
>> Here are slide from a talk about the method:
>> http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf
>> And here is a tutorial:
>> http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf
>> 
>> I am sure that you could use GROMACS to do the simulated annealing step
>> instead of NAMD.
>> 
>> Tom
> 
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