Hi,
Unfortunately the 'contacts' command only looks for distances within a
single mask. The only way I can see you doing what you want right now
is to define some distance contacts via visual inspection, write the
distances out to a single file, then post-process that file with a
script, e.g.:
distance d1 <protein mask 1> <ligand mask 1> out distances.dat
distance d2 <protein mask 2> <ligand mask 2> out distances.dat
distance d3 <protein mask 3> <ligand mask 3> out distances.dat
Then distances.dat will contain 4 columns; an index column (frame #)
and the 3 distances. Then you can process with a script, e.g.
awk -v cutoff=<CUTOFF> '{
if ($1 != "#Frames) {
Ncontacts = 0;
for (col = 2; col <= 4; col++) {
if ($col < cutoff)
Ncontacts++;
}
printf("%i %i\n", $1, Ncontacts);
}' distances.dat
The ability to use two masks in 'contacts' would be ideal though; I'll
put it on my to-do list. Thanks!
-Dan
On Mon, Aug 26, 2013 at 12:20 AM, anu chandra <anu80125.gmail.com> wrote:
> 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
>> > _______________________________________________
>> > 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 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> 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 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 Tue Aug 27 2013 - 10:00:02 PDT
