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,
Antoine
________________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
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.
http://q4md-forcefieldtools.org/REDServer-Development/
See q4md-forcefieldtools tutorials as well:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
involving multiconformation and multiorientation RESP/ESP fit for
whole molecule and molecular fragments (amino-acid case):
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25
--
I ran a test for you using the 2 conformations of ethanol in three
different inputs using R.E.D. Server Dev./PyRED:
See
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231.html
in agreement with data in REDDB:
http://q4md-forcefieldtools.org/REDDB/projects/W-10/
PyRED inputs provided to the PDB file format:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Project.config
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:
Conformation_anti
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m1/input1-sm_m1.in
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m1/input2-sm_m1.in
Conformation_gauche
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m2/input1-sm_m2.in
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m2/input2-sm_m2.in
Conformations_anti+gauche
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/input1-sm_m3.in
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/input2-sm_m3.in
All together (not that useful in your case)
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/input1_mm.in
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/input2_mm.in
You get the corresponding FF libraries (with charges, topology and FF
atom types):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m2/Mol-sm_m2-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/Mol-sm_m3-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/Mol-sm_m3-c2.mol2
and
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/Mol_mm1-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/Mol_mm2-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/Mol_mm3-c1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_MM/Mol_mm3-c2.mol2
You get also frcmod files:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
a leaprc script:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Data-Default-Proj/leaprc.q4mdfft
to directly execute the LEaP program
and energy values:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m1/Energy_m1-c1.txt
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m2/Energy_m2-c1.txt
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/Energy_m3-c1.txt
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnWoCcKzVADFInFgm09PXua0n5ecPg9Fn1/P7231/Data-R.E.D.Server/Mol_m3/Energy_m3-c2.txt
etc, etc...
Then considering which conformation(s) to be involved in the charge
fit procedure you can find many pieces of information in:
http://pubs.acs.org/doi/abs/10.1021/ja00049a045?journalCode=jacsat
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
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
potentials
- 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:
http://q4md-forcefieldtools.org/REDServer-Development/resp/
- 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:
http://q4md-forcefieldtools.org/REDServer-Development/popup/popkeyword.php
I hope this helps,
regards, Francois
Quoting "Marion, Antoine" <antoine.marion.tum.de>:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Nov 24 2016 - 06:00:03 PST
