Re: [gmx-users] binding sites with MD

Gesendet:Samstag, 24. Mai 2014 um 12:24 Uhr Von:Nidhi Katyal nidhikatyal1...@gmail.com An:Discussion list for GROMACS users gmx-us...@gromacs.org Betreff:[gmx-users] binding sites with MD Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites

[gmx-users] binding sites with MD

Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns,

Re: [gmx-users] binding sites with MD

On 5/24/14, 6:24 AM, Nidhi Katyal wrote: Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially.

Re: [gmx-users] binding sites with MD

Look for papers by D. E. Shaw and Gianni di Fabritiis. They have done this, but it generally takes at least microseconds or milliseconds to converge. On Sat, May 24, 2014 at 6:24 AM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all, I would like to ask if unbiased MD in nanoseconds time

Re: [gmx-users] binding sites with MD

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

Re: [gmx-users] binding sites with MD

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?

Re: [gmx-users] binding sites with MD

Vmd can convert trajectories, as can other tools. Google is your friend! Sent from my iPhone On May 24, 2014, at 15:13, Albert mailmd2...@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

Re: [gmx-users] binding sites with MD

I know that. But none of this tool is perfect and they are always this or that problem. It would be better if this tool can natively support Gromaccs. thx Albert On 05/24/2014 11:00 PM, Michael Shirts wrote: Vmd can convert trajectories, as can other tools. Google is your friend! Sent from