Hi Dave,
Thanks for the answer and the interesting discussion.
The choice of charge model (polarizable or not) is indeed a crucial point.
However, at the moment I am more focused on the theory behind RESP.
I will make such choices later.
I might clarify my questions:
- How the weight of each conformation is accounted for during RESP fitting?
- Why do the following two settings of RESP give different results?
a) single conformation (confA)
b) two conformations (confA and confB) with the weight of confA and confB set to 1.0 and 0.0, respectively.
- What is your opinion regarding the use of a simple average of confA and confB charges instead of multiconformation RESP?
Thanks again for your help.
Best regards,
Antoine
________________________________________
From: David Cerutti [dscerutti.gmail.com]
Sent: Wednesday, November 23, 2016 5:27 PM
To: AMBER Mailing List
Subject: Re: [AMBER] About multiconformations RESP fitting
I don't think that a simple averaging is quite what you'd get if you were
to fit both conformations simultaneously, equally weighted. But, it's also
not surprising that you get very different results by fitting to both as
opposed to just the one. REsP is more stable than its boisterous cousin
ESP, but there is still a high dependence on the input conformations. When
I fitted charges for amino acids, I took twenty conformations of each of
them (500 conformations across twenty amino acids plus other protonated
forms--it was a big matrix problem). Much of this depends on how flexible
and polarizable your system is. If there is a high degree of electronic
polarization, then there could be a problem making a fixed charge model at
all, but in general if the molecule is flexible you're going to expose
different surfaces with different conformations, which will implicitly
weight the importance of particular charges differently, so even if there
is no polarization a flexible molecule will have conformational dependence
in REsP fitting which can only be removed by sampling.
Dave
On Wed, Nov 23, 2016 at 10:39 AM, Marion, Antoine <antoine.marion.tum.de>
wrote:
> Dear Amber community,
>
> I am trying to reach a better understanding of the RESP procedure.
> In particular, I am interested in multiconformations RESP fitting.
>
> I have followed the explanations of the tutorial (
> http://ambermd.org/tutorials/advanced/tutorial1/section1.htm)
> and adapted it to my problem (modified alanine dipeptide).
> The programs are running well and after a few corrections of inputs, I get
> results that seem very reasonable.
>
> My concern is about the theory behind.
> I understood (by trying) that the way in which the different conformations
> are taken into account is not a simple average.
> Then, I tried to vary the weight of each conformation (say confA and
> confB).
> To my surprise, when setting the weight of confB to zero, I get a (very)
> different result than when I do a RESP fitting on confA only.
> I might have miss one equation, but I could not find where the weighting
> factors are used.
>
> I would greatly appreciate some directions to understand this matter.
>
> Another question:
> Would a simple average of the atomic charges (weighted or not) be also
> acceptable to account for both conformations?
>
> Thanks in advance.
>
> Best regards,
> Antoine MARION
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 23 2016 - 09:30:02 PST
