Hi Tyler,
Thank you very much for your reply - it was really helpful.
Following what you said, I moved my protein so that it will be at the center of a box starting from (0,0,0) and used centering 0 (the reason is because I want to have exactly the same box for different proteins) but the grid it's not going to start from (0,0,0) as expected; for example in my case is starting at -35 -35 -35 as I specified a box size of 70. I know that at this point I only need to change the "origin" in the dx file to 0 0 0 to have it on top of my protein but I was wondering if that's correct because as far as I understand from your reply it should still build the grid starting from 0 0 0 (?).
Many thanks
Kind Regards,
Lucia
-----Original Message-----
From: Tyler Luchko (Lists) [mailto:tluchko.lists.gmail.com]
Sent: 20 April 2017 19:18
To: AMBER Mailing List
Subject: Re: [AMBER] 3D-RISM centering 0
EXTERNAL
Hi Lucia,
I’m not sure what you are trying to do with ‘--centering 0’. This should be considered an expert setting and is only used in special circumstances. Also, are you using periodic or non-periodic 3D-RISM. Your full command line would help.
The 3D-RISM solvation grid starts at (0,0,0) and goes to (solvbox_x, solvbox_y, solvbox_z). With ‘—centering 1’ the solute center-of-mass is move to the center of this box for the 3D-RISM calculation and then moved back to its original location. Any output grids are appropriately translated to the original location of the solute. This is almost always what you want.
‘—centering 0’ gives you the option to manually place the solute in the solvation box. The solvation grid is still from (0,0,0) and to (solvbox_x, solvbox_y, solvbox_z) but the position of the solute is not changed from its original location. You, as the user, need to provide an input file with the solute positioned exactly as you want with the knowledge of where the solvent grid will be.
The second most popular option is ‘—centering 2’, which translates the center-of-geometery of the solute. This is used for minimization where the center-of-geometry is constant instead of the center-of-mass.
HTH,
Tyler
> On Apr 20, 2017, at 10:05 AM, Lucia Fusani <lucia.x.fusani.gsk.com> wrote:
>
>
> Hi,
>
>
> I am using rism3d.snglpnt (in Amber 16) and when I specify the option
> “--centering 0” as well as the grid size and grid points (--solvbox and –ng)
> I get an unexpected results. See attached picture. I obtained the same
> results with Amber12.
>
> What am I doing wrong and what can I do to fix that? The reason why I want
> centering 0 is because I want to be able to decide the origin of the grid
> that is not possible in any other cases. Any suggestions?
>
>
> Many thanks
>
>
> Kind Regards,
>
> Lucia
>
>
> Lucia Fusani
>
> Industrial PhD Student
>
> Complementary Worker on Assignment at GSK
>
> Molecular Design UK
>
> R&D Platform Technology & Science
>
>
> GSK Medicines Research Centre
>
> Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
>
> Email [1]Lucia.x.Fusani.gsk.com
>
>
> [2]gsk.com | [3]Twitter | [4]YouTube | [5]Facebook | [6]Flickr
>
>
> cid:image001.png.01D0FF8F.1ACF64F0
>
> _________________________________________________________________
>
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GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.
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Received on Wed Apr 26 2017 - 09:00:03 PDT
