Hi,
I have a situation in which my input file contains 12 peptides, which in the PDB are separated by a TER. Now I would like to calculate all kind of parameters like “lie” or “surf” on each of those fragments on the cpptraj analysis file. But without doing it manually.
Is there a way to identify from the .prmtop or the .inpcrd the different molecules I have and thus to identify the numlist mask numbers of each peptides such that I could automatically write syntax like:
#energies of interaction
surf :1-22 out surf1.out
surf :23-44 out surf2.out
surf :45-66 out surf3.out
surf :67-88 out surf4.out
surf :89-110 out surf5.out
surf :111-132 out surf6.out
surf :133-154 out surf7.out
surf :155-176 out surf8.out
surf :177-198 out surf9.out
surf :199-220 out surf10.out
surf :221-242 out surf11.out
surf :243-264 out surf12.out
But again, doing it such that the mask numbers of each pepptide will be idenfied automatically?
At the moment I do it manually for each variant… a lot of manual work.
Best regards,
fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
fglaser.technion.ac.il
Tel: +972 4 8293701
http://bku.technion.ac.il
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
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Received on Thu Sep 10 2015 - 03:30:03 PDT
