I think I got it.
When I did align in Pymol, with my pdb (before minimization) and after minimization, I see that the C3N molecule is present exactly at my point of interest.
I think I made a bad mistake by looking at the coordinates for comparing my C3N molecule location.
If you see the coordinates have changed, but the molecule looks to be tethered at the same point after minimization.
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________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Wednesday, October 16, 2019 9:34:58 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
Everything might be centered on the origin, maybe even axis-aligned. If
you load both, it should look like a true double image if that applies.
Bill
On 10/16/19 6:32 AM, Debarati DasGupta wrote:
> 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.
>
>
>
> Regards
>
>
>
>
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>
>
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>
>
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>
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
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>
>
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Wednesday, October 16, 2019 8:22:46 AM
> To: AMBER Mailing List <amber.ambermd.org>
> 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?
>
> ....dac
>
>
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Received on Wed Oct 16 2019 - 07:00:03 PDT
