Re: [AMBER] About multiconformations RESP fitting

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 25 Nov 2016 09:07:34 +0100

Dear Antoine,
(Marion is also a french firstname, sorry)

Concerning R.E.D. Server Dev. and its limitations:
http://q4md-forcefieldtools.org/REDServer-Development/faq.php#8
http://q4md-forcefieldtools.org/REDServer-Development/faq.php#17
http://cluster.q4md-forcefieldtools.org/qstat/qstat.php

We can postpone all these limits if the user contact us.

We always follow the
queueinghttp://cluster.q4md-forcefieldtools.org/qstat/qstat.php system
and increase/decrease the number of nodes depending on our needs here
and the needs of the R.E.D. Server Dev. users. Also when we see that a
user has many waiting jobs in the queue we modify the PBS rules to
open more simultaneous jobs for that user. All that to tell You that
we can open more than 3 simultaneous jobs for a user if she/he has
many jobs to run for a project. I think we can allow easily more than
80 cores for a user for a defined period of time. Just contact us to
explain your needs.

regards, Francois


> Dear Fran├žois,
>
> 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



           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


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Received on Fri Nov 25 2016 - 00:30:03 PST
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