AMBER Archive (2008)

Subject: Re: AMBER: amber ff and how it deals with out-plane chiral C

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jul 22 2008 - 10:15:56 CDT

I don't know of any all-atom force fields for MD that use impropers for
chirality. you might want them for programs that use extreme conditions
such as annealing (and in fact we typically add them as restraints during
high temperature runs). this is because you might invert chirality with
very large energies, but during normal MD I don't think that can readily happen
because you need to severely distort the bond angles to get it to happen.
you might read the early all-atom force field papers, such as the Cornell et al
reference. these should be in the amber manual.
carlos

On Tue, Jul 22, 2008 at 10:41 AM, Alan <alanwilter_at_gmail.com> wrote:
> Hello Carlos and List.
>
> Thanks for your reply.
>
> I will try to make myself clear.
>
> My experience is with GROMOS ff (let's say G43a1). Ok, it's a united
> atom ff, but it'll suffice for what I want to know. Let's focus on
> PHE.
>
> In Gromos FF, for PHE (and all others amino acids in fact) there's a
> improper out-of-plane describing [CA N C CB], besides of
> couse impropers describing the ring and its planarity.
>
> But in amber ff (i.e., amber 94, 96, 99 and AFAIK 03 too), we don't
> have such improper, only impropers for the ring (to keep it planar),
> i.e., improper dihedral [CA N C CB] is parametrised by a
> set of torsionals ([CA C +N +H], [-C N CA CB],
> etc.)
>
> I can fully understand this way amber does is pretty much OK and I
> didn't say that amber should use improper terms for chiral carbon.
>
> In fact, all I want to know is why Amber took this approach and Gromos
> took another, just this. And for Gromos I can find info in Gromacs
> manual for example.
>
> Besides, I always "knew" too (as you mentioned: as far as I know those
> were only used for united atoms models) that Amber ff (all-atoms) took
> this approach (like opls all-atoms) because once H is there one could
> use torsional to parametrise chiral carbons instead of improper. And
> when I mention "knew" is because I always "heard" (like you did here)
> people saying so but I never "read" a paper or so referencing that.
>
> So, I would appreciate very much if I could have a link/reference
> about why torsional and not improper for chiral carbon in an all-atoms
> ff.
>
> Many thanks again.
> Cheers,
> Alan
>
> PS: As example of a ff with all-atoms representation but also using
> improper for chiral carbon look at "xplor/toppar/protein.top" from
> Xplor-Nih.
>
>
> On Tue, Jul 22, 2008 at 12:57 PM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
>> Hi Alan-
>> why should improper terms be needed for tetrahedral carbon?
>> as far as I know those were only used for united atoms models. in
>> all-atom models, the 3-body angles do a fine job at keep the carbon tetrahedral.
>> maybe it would help us if you specify what you mean by "amber ff",
>> since there are many variations, some all-atom and some united. whether
>> they have impropers or not may depend on which one you mean.
>> certainly the different force fields intendend to be used with Amber
>> have many differences (and similarities of course)
>>
>>
>> On Tue, Jul 22, 2008 at 3:59 AM, Alan <alanwilter_at_gmail.com> wrote:
>>> Hi List!
>>>
>>> I've read "here and there" that Amber FF doesn't use improper
>>> dihedrals parameters for tetrahedral carbon (out-of plane) and for
>>> that a set of torsionals would do the parametrisation.
>>>
>>> Disregarding some likely wrong assertions above, where would I find
>>> further information about this particularity in amber ff? I failed to
>>> find that in Amber manual 10.
>>>
>>> Many thanks in advance.
>>>
>>> Cheers,
>>> Alan
>>> --
>>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>>> Department of Biochemistry, University of Cambridge.
>>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>>>http://www.bio.cam.ac.uk/~awd28<<
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
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>>>
>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Associate Professor Phone: (631) 632-1336
>> Center for Structural Biology Fax: (631) 632-1555
>> CMM Bldg, Room G80
>> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> ===================================================================
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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