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

From: Debarati DasGupta <>
Date: Wed, 16 Oct 2019 13:32:02 +0000

Hello Prof Case,

Yes I have looked at the complex before minimization and after minimization.

Please find my attached input file for leap, my setup.pdb and my minimized.pdb , if that helps to make my question understandable.

My point of interest is C2 atom of C3N molecule should be fixed at -6.000 14.000 -2.500 location.

It moves a lot even after restraining the molecule with 500 restrain weight.

I do not understand why is it so.

Looking to hear back from you.


Sent from Mail<> for Windows 10

From: David A Case <>
Sent: Wednesday, October 16, 2019 8:22:46 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] minimize protein with a small molecule tethered at a fixed location

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 - 07:00:01 PDT
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