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.O3',O4',O5',O1P,O2P
donor mask :ADE.N1,N3,N7
donor mask :THY.O2,O4
acceptor mask :1.O5' :1.H5T
acceptor mask :13.O5' :13.H5T
acceptor mask :12.O3' :12.H3T
acceptor mask :24.O3' :24.H3T
acceptor mask :ADE.N6 :ADE.H61
acceptor mask :ADE.N6 :ADE.H62
acceptor mask :THY.N3 :THY.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.chem.ucsb.edu
phone: x7158
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Received on Wed Apr 13 2005 - 01:53:01 PDT
