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
autoimage
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
acceptable?
Thank you,
sincerely,
Silver
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Received on Sun Jan 18 2015 - 22:00:03 PST
