Re: [AMBER] About multiconformations RESP fitting

From: Marion, Antoine <>
Date: Thu, 24 Nov 2016 13:38:45 +0000

Dear François,

Thanks for this detailed answer.
It is very helpful to have such examples for comparison.
I'll now try to reproduce your examples.

I know the RED server and I already used it for other projects.
I would like to mention how much I appreciate it: Thanks to the team for this great piece of work!

For the project I am currently working on, aside from the other parameters, I have to perform several hundreds charge calculations.
For convenience, it is easier for me to run locally and to control each step myself.
I will follow your advice and keep standard weights (1.0).
I will also make some tests to validate the procedure (single/multi conformations).

Thanks again for your help!

Best regards,

From: FyD <>
Sent: Thursday, November 24, 2016 11:32 AM
To: AMBER Mailing List
Subject: Re: [AMBER] About multiconformations RESP fitting

Dear Marion,

You might try R.E.D. Server Dev./PyRED to run multiconformation
(and/or multiorientation) RESP/ESP fit...
to generate charge values and more generally a force field for
molecules and/or molecular fragments.

See q4md-forcefieldtools tutorials as well:
involving multiconformation and multiorientation RESP/ESP fit for
whole molecule and molecular fragments (amino-acid case):


I ran a test for you using the 2 conformations of ethanol in three
different inputs using R.E.D. Server Dev./PyRED:

in agreement with data in REDDB:

PyRED inputs provided to the PDB file format:
i.e. conformations anti and gauche are considered as two different
molecules: molecules 1 and 2, while 2 conformation RESP fit is carried
for molecule 3

RESP inputs for RESP fit are at:



All together (not that useful in your case)

You get the corresponding FF libraries (with charges, topology and FF
atom types):

You get also frcmod files:
a leaprc script:
to directly execute the LEaP program
and energy values:
etc, etc...

Then considering which conformation(s) to be involved in the charge
fit procedure you can find many pieces of information in:

Finally several/quick comments:
- charge 'fitting' using different conformations/orientations is
different from charge 'averaging' (this can be compared with PyRED as
well; see below the charge models); in short averaging means ones
generates mean values from different sets of charge values while
fitting means one generates a single set of charge values using
different conformations/orientations so different electrostatic
- varying the weights in RESP and using 'non-standard values' in
particular setting zero values might be not implemented or worst
buggy: I would keep standard values... You can also find an updated
RESP version at:
- this is difficult to 'predict' which approach (single or multiple
conformations/orientations) would lead the 'best' results: I would
validate the different force fields generated when using the different
sets of charge values/different fitting procedures.

See the charge models implemented in PyRED:

I hope this helps,
regards, Francois

Quoting "Marion, Antoine" <>:

> 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
> (
> 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
> _______________________________________________
> AMBER mailing list

           F.-Y. Dupradeau

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Received on Thu Nov 24 2016 - 06:00:03 PST
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