Hi, I have a box of molecule A dissolved in water. I want to calculate the dipole moment of the water forming the cage around molecule A (i.e. the first layer of water molecule surrounding molecule A). I tried using cpptraj but I don't think I have what I really want.
In general, I create a script file that contains these lines (1) and (2), and do cpptraj -i dipole.script -p prmtop > output. The commands in the script used:
(1) trajin mdcrd.run1
vector ve1 (:402<:5.0) dipole out fileout
>From what I understood, the :402 should be the residue number of molecule A, <: should give all the residue within, and the 5.0 is the distance. But when I change the value of 5.0 to 10.0, I still get the same dipole vector, thus I don't think I am doing it right.
After a few trials, I just get the error in three separate lines, with no output file written.
"selectDistd(): No coordinate info for distance operator.
Error: selectDistd failed.
Segmentation fault"
(2) trajin mdcrd.run1
vector ve1 [:402<:5.0] dipole out fileout
if I try this, I will just get the error
"Unknown symbol ([) expression when parsing atom mask ([:402<5.0])
parsing atom mask: unknown symbol (?)
Segmentation fault"
Can anyone shed some light on what I am missing here?
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
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Received on Mon Nov 05 2012 - 13:30:02 PST
