Dear Daniel,
Thanks for the reply. As I understood from the manual, the command
'contacts' will check for the number of contacts between the atoms
specified in the mask. For e.g, if the mask is ':.A' , then command
'contacts' will look for number of interactions between all the 'A' atoms
within the specified cut-off distance. But, my system contains 290 amino
acid residues and ligand is the 291-th one. Here I am a bit confused about
creating a mask in such a way that I will get the number of contacts (
heavy atom - heavy atom contacts) ligand (291) make with the protein
(1-290). Can you please help me out?
Many thanks
Regards
Anu
On Fri, Aug 23, 2013 at 9:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Check out the 'contacts' command in CPPTRAJ/PTRAJ. This will determine
> contacts as distances between atom pairs using a mask and a distance
> cutoff based on either a reference frame or the first frame of your
> trajectory. See the AmberTools 13 manual for more details.
>
> -Dan
>
> On Fri, Aug 23, 2013 at 6:44 AM, anu chandra <anu80125.gmail.com> wrote:
> > Dear Amber users,
> >
> > I am working with protein-ligand interaction. I would like to calculate
> the
> > number of contacts ligand make with the protein within a specific cut
> off (
> > say within 3.5 to 4.5 angstroms), along the simulation trajectories. How
> > can I get help from PTRAJ/CPPTRAJ for doing this calculation?.
> >
> > Thanks in advance
> >
> > Regards
> > Anu
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Sun Aug 25 2013 - 23:30:03 PDT
