Re: [AMBER] How to superpose the solvated box to the original pdb structure?

From: Gao Zhenting <>
Date: Tue, 5 Oct 2021 23:49:50 +0800

Hi Dac,

I tested "set default nocenter on" in tleap, but the output solvated
protein coordinates are still different from the original one.
Could you help to check?

Here is the commands I used:
tleap -f
ambpdb -p fxa.prmtop -c fxa.rst7 > fxa_solv.pdb
#compare fxa.pdb and fxa_solv.pdb in PyMOL


David A Case <> 于2021年10月5日周二 下午8:41写道:

> On Tue, Oct 05, 2021, Gao Zhenting wrote:
> >
> >After solvating the protein into a box, the original coordinates of the
> >protein are changed. Is there any way to superpose the solvated system to
> >the original pdb structure, so that it is easier to compare the trajectory
> >with the original pdb conformation?
> You can use "set default nocenter on" to keep tleap from moving the
> coordinates upon setup. But, of course, the system will "drift" as you run
> MD, so something like cpptraj is needed to superpose the system back to the
> original coordinates.
> ...dac
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Received on Tue Oct 05 2021 - 09:00:02 PDT
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