Re: [AMBER] cpptraj SolventAcc and ligand distance plotting

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 18 Apr 2016 08:33:23 -0600

Hi,

On Sun, Apr 17, 2016 at 12:59 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear All,
> I am doing analysis of 5 ns trajectories, which I have run using Amber 14. I have calculated hydrogen bond to track all solute-solute and solute-solvent hydrogen bonds using cpptraj. Now I want to plot the distance between these hydrogen bond vs time.
> SolventAcc THA_533.H13 THA_533.N27 7451 0.2980 2.8909 154.2805
> In above pasted cpptraj hydrogen bond result, solvent is making hydrogen bond with THA (ligand). For running distance command, I will mention 533.N27 for ligand but for solvent Acc I do not know the number. So Kindly tell me how can I able to plot distance vs time for these two ligand and solvent atoms.

This is a hydrogen bond between solute and *any* solvent molecule, so
there is no one specific pair of atoms with which to calculate a
distance. What you could probably do is use the 'closest' command to
keep the closest solvent molecule to :533.N27 and then calculate that
distance.

-Dan

> Thank you.
> Best Regards, Saman Yousuf Ali
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 18 2016 - 08:00:03 PDT
Custom Search