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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> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
>
>
> ________________________________
> 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 - 07:00:02 PDT
