On Fri, Jan 22, 2016 at 7:08 AM, richa anand <richaaanand.gmail.com> wrote:
> Dear Amber users
>
>
> I want to analyze the ligand-receptor interactions through LIE command
> using CPPTRAJ. I have gone through mannual but could not get how to prepare
> input file. I have used the following input file:
>
> trajin *.crd
>
> center origin :1-20
> image origin center
>
I suggest replacing these two commands with "autoimage" instead. Autoimage
almost always just "does the right thing".
> strip : Na+
> strip : WAT
>
LIE is done in explicit solvent. Stripping the solvent here is the wrong
thing to do.
lie ligandmask :20-20
> lie surrounding mask :1-19
> lie cutvdw 12.0 cutelec 12.0 out lie.out
>
You ran three different LIE commands. It looks like you just want to run
one:
lie :20 cutvdw 12.0 cutelec 12.0 out lie.out
Note that "ligandmask" is not a keyword here. The first mask given to the
command *is* the ligand mask. Same for the surrounding mask. "surrounding
mask" are not keywords. And the ligand mask is required. Which means none
of these three commands is valid, and all three should have produced either
warnings or errors that they were being ignored.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 22 2016 - 05:30:03 PST
