On Sun, May 24, 2015 at 7:18 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I’ve used LIE for the first time. My input file was:
>
> parm complex_solv.prmtop
> trajin prod_0-100ns.nc
> lie INT :126 :10,73,76,77,80,84,87-92,111,114,123 out lie.out
> run
> write interactions.agr INT[EELEC] INT[EVDW]
>
> giving
>
> ACTION OUTPUT:
>
> DATASETS:
> 2 data sets:
> INT[EELEC] "INT[EELEC]" (double), size is 10000
> INT[EVDW] "INT[EVDW]" (double), size is 10000
> DATAFILE OUTPUT:
> lie.out: INT[EELEC] INT[EVDW]
> lie.out: Writing 10000 frames.
> [write interactions.agr INT[EELEC] INT[EVDW]]
> INT[EELEC] INT[EVDW]
> interactions.agr: Writing 10000 frames.
>
> I have a couple of questions regarding the output.
>
> 1. Most importantly, shouldn’t the script produce individual interactions
> between the LIGAND and the RESIDUES in the mask?
>
No, it computes one energy -- the one between all atoms in the ligand mask
and all atoms in the "surroundings" mask. It is a double-sum like the
following:
E = sum_i sum_j [ qi*qj/rij + Aij/rij^12 - Bij/rij^6 ]
Where "i" is the set of atoms in the ligand mask (:126) and "j" is the set
of atoms in the surroundings mask (:10,73,76,77,80,84,87-92,111,114,123).
2. Shouldn’t separate INT[EELEC] and INT[EVDW] files be written out?
>
Both data sets are written as separate columns to the same file.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun May 24 2015 - 09:00:02 PDT
