Thank you very much Daniel
I did in similar way as you mention here with small modification.
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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On Fri, Jul 20, 2018 at 8:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Jul 16, 2018 at 6:23 AM, MOHD HOMAIDUR RAHMAN
> <rahmanhpu.gmail.com> wrote:
> >
> > I want to calculate distance between two solvent mask closest to two end
> of
> > a protein. For that I have define two mask, solvent A that is near to
> resid
> > 1 and solvent B near to resid 20.
>
> It's an interesting problem. The issue with your current strip is that
> once the first 'closest' command is processed, you only have 1 water
> (the one closest to :1). So when you get to the second 'closest'
> command, it only has the 1 remaining water to look at. You need to do
> this in two passes - in the first you need to add an 'unstrip' command
> to reset the first 'closest', and save coordinates of just the closest
> waters to your target residues. Then in a second pass you can combine
> those coordinates and calculate the distance. Here's some input I
> tested on a system I have where I determined the distance between the
> closest waters to residues 1 and 12:
>
> # Load topology/trajectory
> parm tz2.ortho.parm7
> trajin tz2.ortho.nc
> # Closest water to residue 1.
> closest 1 :1 parmout closest.01.parm7
> # This will have the water and solute, so strip the solute.
> strip !:WAT
> # Save coordinates of closest water to res 1
> createcrd Closest01
> # Reset 'closest'
> unstrip
> # Now closest water to residue 12
> closest 1 :12
> # Strip out the solute
> strip !:WAT
> # Save coordinates of closest water to residue 12
> createcrd Closest12
> # Run
> run
> # Combine coordinates of the two closest waters
> combinecrd Closest01 Closest12 crdname Combined
> # Calculate distance
> crdaction Combined distance :1 :2 out distance.1.12.dat
> # Uncomment to output combined trajectory for visualization if desired
> #crdout Combined water.1.12.mol2
>
> Hope this helps,
>
> -Dan
>
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Received on Sat Jul 21 2018 - 02:30:03 PDT
