Poojari, Chetan wrote:
Hello Justin,
I wanted to find the probability of hydrogen bond formed between my peptide and
water molecules over time. So I used your plot_hbmap.pl script.
As mentioned in the script file, my index file contained atom numbers only from
the [hbonds...] section, rest were deleted.
Heres my short output after running the script:
# Donor Acceptor % Exist.
0.004
ALAA N 0.004
ALAA N 0.016
ALAA N 0.012
ALAA N 0.008
ALAA O 0.008
ASNA OD1 0.012
GLYA O 0.008
ALAA O 0.008
Please can I know if this is the expected output from the script ??? if not
please can I know what might be wrong in my input ????
This is absolutely not the correct output. Probably your index file is not
correct. Also note that if you want proper residue names/numbers, you need to
use a .pdb file that does not have chain identifiers.
-Justin
Kind regards,
chetan.
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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