From: Sylvester Tumusiime <stumusii.uno.edu>
Date: Mon, 19 Jan 2015 05:44:01 +0000

   Dear Amber members,
   Am trying to determine hydrogen bond formation between my molecule and the
   solvent. I have 3 questions:
   1. I have noticed that when i have autoimage or not, i get different results
   in the SOLVOUTWAT.dat file (see commands below). I am wondering whether or
   not it is important to include autoimage in my commands. This is my setup:
   trajin equil2.netcdf 1 10000 1
   trajin prod.netcdf 1 10000 1
   trajin prod2.netcdf 1 10000 1
   trajin prod3.netcdf 1 10000 1
   trajout Flp.netcdf netcdf
   hbond HBONDWat1 out HBONDWat-N1.dat :1 angle 135 dist 3.0 series
   solventdonor :WAT solventacceptor :1 solvout SOLVOUTWat1.dat
   2. Is it possible to have a look at my set up above and let me know if the
   hbond command is correct. I have noticed that in some instances, the
   SOLVOUTWAT.dat file is empty while in others its not. I read that i can
   substitute water with ions as the solventdonor. I plan to use the above set
   up and am wondering if this would be okay.
   3. Is the placement of the solvent donor and solventacceptor keywords
   Thank you,
AMBER mailing list
Received on Sun Jan 18 2015 - 22:00:03 PST
Custom Search