AMBER Archive (2005)

Subject: AMBER: ptraj, hbond problem

From: Joseph W.Toporowski (jtoporowski_at_chem.ucsb.edu)
Date: Tue Apr 12 2005 - 19:07:35 CDT


Dear Amber community,

I am trying to analyze the ion environment around a simulated
oligonucleotide using the "hbond" facility of ptraj. I followed a
sample input that Dr. Cheatham recently posted on this mail reflector,
but the results I'm getting do not seem to be accurate. No errors or
warnings appear in the output file, but the .dat file that is
generated suggests that there are no ions near the DNA electron donor
atoms, i.e. no results are shown where sodium is the
"solventacceptor". In an effort to troubleshoot the problem, I
cranked up the cutoff distance to 20 A, and still no ions as
"solventacceptors" were seen, which I know cannot be accurate. Using
the "grid" facility of ptraj, a dense ion environment can clearly be
seen around the minor grooves, etc. I was hoping someone could
provide input on where I'm going wrong. If not, is there any other way
to analyze the ion environment in a quantitative way?

My input file is as follows:

-----------------------------------------
trajin dna_at_all_5025.dcd.gz 667 6667

center :1-24 mass origin
image origin center familiar

prnlev 2

donor mask :1-24_at_O3',O4',O5',O1P,O2P
donor mask :ADE_at_N1,N3,N7
donor mask :THY_at_O2,O4

acceptor mask :1_at_O5' :1_at_H5T
acceptor mask :13_at_O5' :13_at_H5T
acceptor mask :12_at_O3' :12_at_H3T
acceptor mask :24_at_O3' :24_at_H3T
acceptor mask :ADE_at_N6 :ADE_at_H61
acceptor mask :ADE_at_N6 :ADE_at_H62
acceptor mask :THY_at_N3 :THY_at_H3

donor print
acceptor print

prnlev 0

hbond series h1 time 0.75 distance 4.0 out hbond_ions.dat \
solventdonor SOD SOD \
solventacceptor SOD SOD SOD

go
------------------------------------------

Thank you,

Joe Toporowski

email: jtoporowski_at_chem.ucsb.edu
phone: x7158
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