Dear amber experts,
I need something likely trivia, I would like to compute the distances between all heavy atoms for a trajectory, I know the matrix command and nativecontacts and the distance command, but I cannot find a way to write a simple output file with the distance and the residues and atoms number. I would like just a list of distances such as in the matrix output, but also with the atoms and residue information.
The closest I have got is something like this in cpptraj
for atoms A1 inmask :1-3.CA i=1;i++
for atoms A2 inmask :11-13.CA j=1;j++
distance d$i-$j $A1 $A2 out disttest.dat
done
done
Which produces this output, which is ok but without atom and residue names.
#Frame d1-1 d1-2 d1-3 d2-1 d2-2 d2-3 d3-1 d3-2 d3-3
1 32.2327 33.8066 37.2180 28.7986 30.2049 33.5724 25.4904 27.1052 30.5854
2 32.1887 33.7961 37.2363 28.7261 30.1656 33.5574 25.3776 27.0302 30.5366
3 32.2772 33.7814 37.1983 28.7651 30.1107 33.4764 25.4585 26.9877 30.4648
And I would like something like this, or anything similar, that I could later post process.
#Frame 1.CA_10.N 45.O-49.C 62.O-76.CA
1 28.6364 5.5108 29.3293
2 28.6018 5.5183 29.2723
3 28.6502 5.6173 29.2326
4 28.7011 5.5852 29.6333
I also would like to give a cuttoff for the values, such as only those atoms within a certain distance will be writtein out.
Could anybody kindly help me?
Thanks!!
Fabian
----------------------------------------------------------------------------
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 24 2021 - 07:30:02 PDT
