Thank you very much.
I will look into it.
Best,
Aseel
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.edu]
Sent: Saturday, August 12, 2017 4:23 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Cpptraj to center molecules
I am not an autoimage user. Maybe it can do what you want, if you read the
manual, but taking its apparent requirement for a single molecule, maybe
there is no point speculating whether it would figure out how you would like
>1 anchor molecules positioned with respect to each other.
The default would be to take the initial relative positions. Or an iterative
approach may work.
If you know how to program, see the list history for my idea for a
general-purpose algorithm, and on the same thread is some informed advice on
how to use the existing feature, that might help.
Bill
On 8/12/17 1:13 PM, Aseel Bala Ahmed wrote:
> Oh so it would create the bond between the two original molecules
> (across the box) rather than the nearest image?
> I am reluctant to do this because I need the approach to be done in "mass"
> to a large amount of clusters. If this 'interesting' approach requires
> visualization (or anything that requires human judgement), I won't be
> able to apply it in these quantities.
>
> Hmm, would you mind explaining why
> - autoimage origin anchor:4
> - center :4,5 origin
>
> Isn't ideal? Would it not do what I want it to do?
>
> Thanks so much,
> Aseel
>
> -----Original Message-----
> From: Bill Ross [mailto:ross.cgl.ucsf.edu]
> Sent: Saturday, August 12, 2017 4:04 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Cpptraj to center molecules
>
> I'm not recommending this, but an interesting hack would be to create
> a forceless bond between the two molecules of interest, to fool autoimage.
> But with this approach, and no matter how you achieve the effect, you
> will have to settle for the initial relative positions of the two
> molecules, which may not always be what you want.
>
> Bill
>
>
> On 8/12/17 12:55 PM, Aseel Bala Ahmed wrote:
>> Neat!
>> However, would this center only molecule 4?
>> I am looking to center the entire hydrogen bonded cluster (i.e.
>> molecules 4 and 5prime).
>>
>> When I use: autoimage origin anchor :4,5 I get an error:
>> Error: Anchor mask [:4,5] corresponds to 2 mols, should only be 1.
>>
>> Which tells me I could only use the command with one molecule.
>>
>> Would a way around this be to use
>> autoimage origin anchor:4
>> center :4,5 origin
>>
>> to first wrap and find images and then center the whole cluster?
>>
>> Thanks very much for your help.
>> Best,
>> Aseel
>>
>> -----Original Message-----
>> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
>> Sent: Saturday, August 12, 2017 1:50 PM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Cpptraj to center molecules
>>
>> Hi,
>>
>> On Fri, Aug 11, 2017 at 3:36 PM, Aseel Bala <balaahme.msu.edu> wrote:
>>> However, I am running into an issue when 4 is on one edge of the
>>> frame and 5 is on the other edge. In these situations, 4 is actually
>>> H-bonded to an 'image' of 5 produced by the periodic boundary
>>> condition. Let's call this image 5prime.
>> What you are describing is an imaging artifact, and is very common in
>> MD simulations with PBC and coordinate wrapping. The 'autoimage'
>> command was designed to handle this kind of situation. Instead of
'center'
>> and 'image', try:
>>
>> autoimage origin anchor :4
>>
>> Hope this helps,
>>
>> -Dan
>>
>> PS - FYI the 'hbond' command in cpptraj now handles imaging natively
>> via the 'image' keyword.
>>
>>>
>>> In this case, cpptraj actually centers 4 and 5 instead of 4 and 5prime.
>>>
>>>
>>>
>>> Is there a way that cpptraj can be used to center a molecule and the
>>> closest image of another molecule to it? So that I would be able to
>>> have 4 and 5prime in the center?
>>>
>>>
>>>
>>> Thank you very much in advance!
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> Aseel M. Bala
>>>
>>> Michigan State University
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
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>>> QX_wrQuVQ3g&m=20LfRjbPT5pG45UMK4hwAELKL8JMnHCY6shlM8F3YMc&s=2VwOyV3A
>>> 3
>>> d
>>> 5ORrRFvnH2briLHIegcR6PBQ-6H8Ep4cA&e=
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.lobos.nih.go
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>> _lcb&d
>> =DwICAg&c=nE__W8dFE-shTxStwXtp0A&r=-GD698Wi4V6QX_wrQuVQ3g&m=20LfRjbPT
>> 5
>> pG45UM
>> K4hwAELKL8JMnHCY6shlM8F3YMc&s=R2gD4ypDg64becFQ8KfNyqAgaRdMD-aZTsg64Ck
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Received on Sat Aug 12 2017 - 15:00:03 PDT
