On Mon, Jun 24, 2019, Sadaf Rani wrote:
>
>protein = loadPdb "Combined_nolig.pdb"
>complex = combine {protein ligA ligB}
>protein = createUnit Combined_nolig.pdb
This isn't doing what you probably think: "createUnit" creates a new and empty
unit with the name protein. This overwrites (I think--I hardly ever use this
command) your earlier definition of "protein".
>setBox protein "vdw"
This is not needed, since the next command sets the box anyway.
>solvateBox protein TIP3PBOX 14.0 iso
>addIonsRand complex Na+ 0
Is this what you want? You used "solvateBox" on "protein", but "addIonsRand"
on "complex".
Approach I recommend: avoid commands like combine and createUnit. Prepare by
hand a single pdb file with everything you want in it, then use a single
loadPdb command to create the unit.
>Running: /home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o sqm.out
>/home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
>Cannot properly run "/home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o
>sqm.out".
The intention is for you to look in the sqm.out file to see what the problem
might be. (Scott: can this get added to the message?)
Note that parameterizing anions (and especially phosphates) are difficult, and
often require hand-preparation.
....dac
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Received on Mon Jun 24 2019 - 19:00:02 PDT
