AMBER Archive (2005)

Subject: Re: AMBER: Ptraj and order of operations

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Wed Jul 13 2005 - 02:21:48 CDT

Hello Kristina,

>>>trajin test.crd 2 2
>>>reference test.pdb.1
>>>trajout pass.pdb pdb
>>>image center familiar
>>>rms first out rmsCheckPass :554
>>>go

>>>trajin test.crd 2 2
>>>reference test.pdb.1
>>>trajout fail.pdb pdb
>>>rms first out rmsCheckFail :554
>>>image center familiar
>>>go

rms fits selected residues by rotation of system. It means that also box
is rotated. However image only works with original box orientation.

So the corect order of actions is to perform image first and then rms.
Therefore the second script is incorrect.

If you use the second script then it can happen, in worst case, that
solute will be overlaped with solvent. The introduced error only depends
on how much the system is rotated by rms.

Example script in amber manual is just example that works only and only
if the system contains one solute molecule, water, and no counterions.
Since the water is removed at the end, the error introduced by incorrect
order of rms and image is eliminated.

Best regards,
        Petr

PS:
if you want to use reference coordinates then you have to use

rms reference out rmsCheckFail :554

Furse, Kristina Elisabet wrote:
>>Simple answer is yes. With the exception of trajin and trajout each
>>action specificied is applied sequentially to the coordinates in the
>>order listed by the user in the input file (courtesy of the AMBER
>>manual).
>
>
> The example input script in the ptraj section of the manual suggests to rms fit,
> then center, then image, so that's what I've typically done. Just thinking
> theoretically it seems safer to image first, then rms fit. That way all of the
> little stray molecules go back in the main box, and then the entire box is
> shifted according to the rms fit. If you do it the other way, rms fit, then
> image, I guess some of the solvent will stay in the same box image, while some
> may move to a neighboring one. But if everything moves the same, they should
> image back the same, right?
>
> I should say I ran into this issue because I strug together 200 restart files
> spanning a 10 ns trajectory so I could get a feel for the whole thing in one
> mddisplay session. I didn't use iwrap, so I have solvent that moves many virtual
> boxes away from the main one by the end of the trajectory. I found that if I
> used ptraj to rms fit the protein backbone first to get rid of rotational
> motion, then imaged (manual-approved protocol and my usual plan), I got a
> trajectory that started out "normal", but as it went along I had solvent
> molecules overwhelming my active site, passing directly through protein atoms. I
> know that didn't really happen in the simulation, so it must be an imaging
> issue, one that is possibly exacerbated as solvent moves farther away. I noticed
> that if instead, I imaged first then rms fit, I got a "normal" looking
> trajectory, with well-behaved solvent. Couldn't find a simple correlation
> between solvent residue number or even x,y,z position and "bad" imaging. Like I
> said before, some of the solvent is imaged properly using the standard order of
> operations, some is not.
>
> Anyway, this might be a situation not many people will run into, and the easy
> workaround seems to be just to image first, then rms fit. But it is weird and
> stuck in my head, and I've already wasted a day of Chris Moth's time looking at
> this when I though it was an mddisplay issue... Any ideas appreciated!
>
> Kristina
>
>
>>On 7/11/05, Furse, Kristina Elisabet <kristina.e.furse_at_vanderbilt.edu>
>>wrote:
>>
>>>Hi-
>>>
>>>Should the order of operations matter for the rms and image commands in
>>
>>ptraj?
>>
>>>For instance, in theory should the following two scripts output the same
>>>coordinates?
>>>
>>>trajin test.crd 2 2
>>>reference test.pdb.1
>>>trajout pass.pdb pdb
>>>image center familiar
>>>rms first out rmsCheckPass :554
>>>go
>>>
>>>trajin test.crd 2 2
>>>reference test.pdb.1
>>>trajout fail.pdb pdb
>>>rms first out rmsCheckFail :554
>>>image center familiar
>>>go
>>>
>>>
>>>I ask b/c I have run into a situation where the above scripts give pdb's
>>
>>which
>>
>>>have coordinates for solvent and counterions that are partly identical and
>>>partly different--for instance, 8 out of 12 Na+'s have identical
>>
>>coordinates in
>>
>>>the two pdb's, while 4 have different coordinates. The system is a protein
>>
>>in a
>>
>>>periodic box. I can give more detail on the problem and system, and my
>>
>>labmate
>>
>>>Chris can talk code, but I thought I'd start with the simple question in
>>
>>case
>>
>>>there was a simple answer...
>>>
>>>Thanks,
>>>Kristina
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>>
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>
>
>
> -----------------------------------------------------------------
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> Email: kristina.e.furse_at_Vanderbilt.Edu
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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> 

-- 
##################################################
   Petr Kulhanek
  ------------------------------------------------
   kulhanek_at_chemi.muni.cz
  ------------------------------------------------
   National Centre for Biomolecular Research
   Masaryk University Brno
   Kotlarska 2, CZ-611 37 Brno
   Czech Republic
##################################################
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