Re: [AMBER] minimize protein with a small molecule tethered at a fixed location

From: David A Case <>
Date: Wed, 16 Oct 2019 08:22:46 -0400

On Tue, Oct 15, 2019, Debarati DasGupta wrote:

>I have a 286 residue protein and I have a acetonitrile molecule and
>TIP3P waters. Now I want my acetonitrile molecule tethered to a fixed
>x,y,z location. SO I deleted the x,y,z coordinates of the C2 atom
>(central Carbon) of ACN and plugged in my x,y,z values. Then I did a
>transformation in Pymol to put everything in the same reference frame.

This last sentence is hard to understand, and we don't know what pymol
has done. Have you (a) looked visually at the complex before
minimization? (b) looked at the ACN coordinates, after pyMol but before
minimization? Do they match the the "before minimization" coordinates
you gave? (c) visually looked at the complex after minimization? Is
the ACN in the proper location relative to other parts of the system?

A 500 kcal/mol restraint will keep your residue from moving. My best
guess is that there is some operator error here: are you sure that the
ACN coordinates in the "-ref" file are really a lot different from the
ones in the restart file after Amber minimization?


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Received on Wed Oct 16 2019 - 05:30:03 PDT
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