Dear amber users,
I've been working with cpptraj in ambertools, the version of cpptraj is
13.24
What i wanna do is to count the bridging waters between DNA and an
enzyme, to do so, i was trying to use bridgeout in cpptraj, but i've
been having some problems.
First of all, if I run my analysis through:
hbond donormask :2-395&.N*,O* acceptormask :396-415&.N*,O* nointramol
out Hbond_enzima_dador.dat dist 3.2 angle 140 avgout
Avg_enzima_dador.dat solvout Solv_enzima_dador.dat bridgeout
Bridge_enzima_dador.dat solventdonor :WAT solventacceptor :WAT&.O
Where, donormask :2-395&.N*,O* is the enzyme donnor atoms
and acceptormask :396-415&.N*,O* is the dna acceptor atoms, bridgeout
still counts bridging waters between enzyme-water-enzyme, and dna-water-
dna, apart from counting enzyme-water-dna.
I can see this in the output file of bridgeout as the number of residues
which are involved with a bridging water appear.
Am I right?
Am i failing to make my selections?
Is there a way to count only the waters involved in bridges between dna
and enzyme (only enzyme-water-dna)?
Also, if i define my selection with same input but trying to count
everything, like as follows:
hbond donormask :2-415&.N*,O* acceptormask :2-415&.N*,O* out Hbond2.dat
dist 3.2 angle 140 avgout Avg2.dat bridgeout Bridge.dat solventdonor
:WAT solventacceptor :WAT&.O
where my selection :2-415&.N*,O* tries to take into account that enzyme
or dna can act as donnor or acceptor, and count everything in one
analysis, my calculation fails and give me the error of segmentation
fault
I've noticed that if you decrease the number of residues involved (i.e.
:2-215&.N*,O* both for donnor and acceptor) the programme works.
I guess it has to do with allocation of memory or something related...
any help would be apriciated
thank you very much
--
********************************
Juan Aranda Moratalla
Phd Student
Laboratorio de Efectos del Medio
Universidad de Valencia
********************************
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Received on Thu Mar 20 2014 - 14:30:02 PDT
