Hi,
First of all, when you reply please do not include the entire contents
of the Amber mailing list digest. It makes your message unnecessarily
long and cluttered.
On Wed, Apr 20, 2016 at 12:46 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> > cpptraj.in
> =============
> parm complex.prmtop
> trajin md_simulation1.mdcrd
> trajin md_simulation2.mdcrd
> trajin md_simulation3.mdcrd
> trajin md_simulation4.mdcrd
> trajin md_simulation5.mdcrd
> center :1-533
> image center familiar
Instead of center/image, try using autoimage.
> strip :Na+
> closest 10 :THA first closestout THA.closestmols.dat outprefix closest
> trajout THA_closestWAT.mdcrd trajectory
>
> THA in above pasted script is my Ligand name. As a result, I got three files: closest.complex.prmtop, THA_closestWAT.mdcrd (trajectory and topology with closest 10 water molecules around mask THA) and THA.closestmols.dat (solvent molecule information). When I load this promtop and trajectory files in vmd, it shows bad clashes between ligand protein and water molecules. What is the reason of this issue? Bad clashes Picture is attached here.
There was no picture attached, but the most common reason for clashes
after imaging is if you have previous performed RMS fitting on the
input trajectory - is that the case? If so you'll need to use the
original trajectory instead (i.e. the one without RMS fitting).
>
> In THA.closestmols.dat file, Mol is (Original solvent molecule number) and First Atm is (First atom number of original solvent molecule.) so what is 6, 3, 4 and 5 represents in the following contents:
Since those numbers are in the Mol column, they represent the original
solvent molecule number.
>
> I wanted to plot distance between my ligand and active site water molecule throughout the production. I don't understand how the closest script help me to track closest water molecule aound my ligand. Is there anything wrong here? I m confused. Kindly help me to encounter this problem.
You need to replace the :THA mask in your 'closest' command with one
that selects atoms that are in/around your active site and only keep
the single closest water.
-Dan
--
-------------------------
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)
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Received on Wed Apr 20 2016 - 13:30:03 PDT
