AMBER Archive (2009)

Subject: Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Thu Apr 23 2009 - 09:30:07 CDT

Dear Karl,

naturally some new reparametrisation of given parameters in this
particular context
is the best choice but I think that the below suggested is also not so bad
regarding to given purpose. I will try and I'll see :)) Of course the
comparison
with experiment will be clear indication if the given solution is enough
for given
purpose or not ...

Best,

   Marek

Dne Thu, 23 Apr 2009 15:54:14 +0200 Karl Kirschner
<kkirsch_at_scai.fraunhofer.de> napsal/-a:

> Hi Marek,
>
> Your solution is as good as any. I must reiterate my caution of
> creating a
> new force field via the Frankenstein method. Each force field that is
> developed has been done so in a specific and unique manner. Since there
> are
> several possible parameter solution for any given force field term, and
> the
> fact that these terms are usually dependent (coupled) upon other terms
> in the
> force field, combining them in this manner can lead to
> unpredictable/unreliable behavior.
>
> I have used this method myself, but on fairly rigid systems where I
> don't
> expect much flexibility to occur during the dynamics. I have also
> validated
> the resulting parameters the best I could by comparison to some
> experimental
> known observable.
>
> Cheers,
> Karl
>
> On Thursday 23 April 2009 15:41, Marek Malý wrote:
>> Dear Karl,
>>
>> thanks a lot again !
>>
>> There is obviously one last question:
>> Where to take the numbers for a "new" gaff
>> terms n3-CG, n3-CG-CG , n3-CG-CG-CG ...
>>
>> One of the natural solutions is in my opinion this:
>>
>> n3-CG = n3-c3
>> n3-CG-CG = n3-c3-c3
>> n3-CG-CG-CG = n3-c3-c3-c3
>>
>> etc.
>>
>> If I am wrong, please correct me, otherwise do not waste time.
>>
>> Thanks for all !
>>
>> Best,
>>
>> Marek
>>
>>
>>
>>
>>
>> Dne Thu, 23 Apr 2009 13:43:31 +0200 Karl Kirschner
>>
>> <kkirsch_at_scai.fraunhofer.de> napsal/-a:
>> > Hi Marek,
>> > Attempted answers below :) .
>> >
>> > On Wednesday 22 April 2009 04:31, Marek Malý wrote:
>> >> Dear Karl,
>> >>
>> >> thanks again !
>> >>
>> >> It seems to me a little more complicated than on the start :)) but I
>> am
>> >> not going to gave up it yet.
>> >> In any case I can always use the "cheaper" alternative with using
>> GAFF
>> >> for dendrimer and also for my bonded maltose, although the maltose
>> >> topology
>> >> will not be probably optimal in this case ...
>> >>
>> >> OK so back to our little complicated story:
>> >>
>> >>
>> >> #1
>> >> Conversion of GAFF atom types to GLYCAM ones in generated prepin
>> files
>> >> couldn't be problem however also here could be some small
>> unclearnesses
>> >> for example to convert c3 I have two possibilities c3->CG or c3->CT .
>> >> CG and CT has the same description ( "sp3 C aliphatic" ) in
>> >> Glycam_06c.dat
>> >> so
>> >> what is the difference between them ?
>> >
>> > As you know c3, CT, and CG are all atom types that refer to sp3 C
>> > aliphatic.
>> > These differences occur because each parameter set was derived in a
>> > unique
>> > way. Giving them different atom names help to maintain that parameters
>> > from
>> > each force field do not overwrite the other's parameters. For Glycam,
>> by
>> > changing only the sp3 C aliphatic atom type, we could ensure that all
>> of
>> > Glycam parameters do not overwrite any protein or rna/dna parameters
>> if a
>> > user wishes to model a mixed bio system.
>> >
>> >> #2
>> >> The most problematic point I see here on the "ff discontinuity" which
>> >> you
>> >> mentioned in your last email. I am not sure if I understood perfectly
>> >> what is necessary to do to solve this problem. So I illustrated
>> >> my understanding in attached picture. Please let me know if I am
>> >> following your ideas in the right manner or not.
>> >
>> > Your illustration represents this idea for the particular bond in
>> > question,
>> > but there are also a few angle bending (~4 terms) and several torsion
>> > terms
>> > (maybe 7 or so) that will need attention.
>> >
>> >> If yes please let me know if I forgot for some parameters which
>> >> should be also add/change to/in gaff.dat and also maybe in some other
>> >> amber files (problem of dependencies) also regarding to later MM-PBSA
>> >> analysis etc.
>> >
>> > I think you are forgeting the angle and torsion terms involving
>> hydrogen
>> > atoms, plus n3-CG-CG-OH
>> >
>> >> #3
>> >>
>> >> What is the difference between files glycam04.dat, glycam04EP,
>> >> Glycam_06.dat, Glycam_06a.dat,
>> >> Glycam_06b.dat , Glycam_06c.dat , Glycam_06d.dat , Glycam_06e.dat ,
>> >> Glycam_06f.dat ?
>> >
>> > The difference between glycam04.dat, glycam04EP is the existence of
>> Extra
>> > Points that resemble lone electron pairs. The differences between the
>> > rest
>> > are just new versions of the force field where some parameters have
>> been
>> > changed to hopefully correct an error in the force field.
>> Glycam_06.dat
>> > and
>> > Glycam_06a.dat are the originals and Glycam_06f.dat is the most
>> recent in
>> > your list. You can access the most recent Glycam force field files at
>> > http://glycam.ccrc.uga.edu
>> >
>> > Cheers,
>> > Karl
>> >
>> >> Thanks in advance for your comments or of course for comments of
>> anybody
>> >> else !
>> >>
>> >> Best,
>> >>
>> >> Marek
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Dne Tue, 21 Apr 2009 09:24:18 +0200 Karl Kirschner
>> >>
>> >> <kkirsch_at_scai.fraunhofer.de> napsal/-a:
>> >> > Hi Marek,
>> >> >
>> >> > I believe that Glycam_06 possesses the necessary parameters for
>> your
>> >> > broken
>> >> > glucose ring residue (maltose already has a prep file). However,
>> and I
>> >> > forgot
>> >> > to mention this, you will have to develop a prep file for this new
>> >> > residue
>> >> > and the appropriate charges that are used with Glycam_06. You can
>> use
>> >> > antechamber to create a prep files for the broken glucose ring
>> >>
>> >> residue,
>> >>
>> >> > using
>> >> > the gaff force field, and then modify the atom types by hand to be
>> >> > Glycam_06
>> >> > atom types. The charges can be computed using the Resp algorithm
>> in a
>> >> > traditional sense as published in many papers (see J. Phys. Chem.
>> 97,
>> >> > 10269
>> >> > (1993); J. Am. Chem. Soc. 117, 5179-5197 (1995)) or using the newer
>> >> > R.E.D.
>> >> > technique (http://q4md-forcefieldtools.org/RED/).
>> >> >
>> >> > In general, note that when you use Gaff with one of the
>> >> > protein/rna/glycam
>> >> > force fields/prep files, and there are covalent bonds between the
>> >> > segments
>> >> > that you want to model using the different force fields, you will
>> >>
>> >> have to
>> >>
>> >> > modify by hand the Gaff parameters so that the terms contain
>> uppercase
>> >> > letters to correspond to the prep files in amber's residue database
>> >> > ($AMBERHOME/dat/leap/prep). Otherwise, in the areas where these
>> >>
>> >> residues
>> >>
>> >> > link
>> >> > together you will have problems getting leap to assign the
>> parameters.
>> >> >
>> >> > I am not sure that parmchk can currently check for correct
>> glycam_06
>> >> > parameters. You will have to do this by checking the files
>> visually if
>> >> > you
>> >> > want to use glycam_06.
>> >> >
>> >> > Cheers,
>> >> > Karl
>> >> >
>> >> > On Tuesday 21 April 2009 05:52, Marek Malý wrote:
>> >> >> Dear Karl,
>> >> >>
>> >> >> thanks again ! If I understood well it is possible to use
>> GLYCAM_06
>> >>
>> >> ff
>> >>
>> >> >> for parametrisation of my "arbitrary" carbohydrate residuum so
>> easy
>> >> >> like to use GAFF forcefield for this purpose. And moreover
>> GLYCAM_06
>> >> >> contains
>> >> >> already big library of common carbohydrates in "Glycam_06.prep".
>> >> >>
>> >> >> If I am not wrong in this general assumption I have one more
>> question
>> >> >> for
>> >> >> you ( hopefully really last one in this story :)) )
>> >> >>
>> >> >>
>> >> >> OK, if I need to parametrise my dendrimer residui (i.e. "central",
>> >> >> "repetitive" and "end" building units)
>> >> >> I just use ANTECHAMBER for creation of the relevant prepin files
>> >>
>> >> which
>> >>
>> >> >> contains GAFF atom types.
>> >> >>
>> >> >> If the analogous way could be used for parametrisation of
>> >>
>> >> carbohydrate
>> >>
>> >> >> residuii using GLYCAM_06 ff
>> >> >> how to force ANTECHAMBER to ("disable" GAFF ff) and generate
>> PREPIN
>> >>
>> >> file
>> >>
>> >> >> of my carbohydrate residuum
>> >> >> (for example my maltose with one broken glucose ring) with
>> GLYCAM_06
>> >> >> atom types (not GAFF ones ) ? and also to force consecutively
>> PARMCHK
>> >> >> routine to check/associate
>> >> >> GLYCAM_06 and not GAFF forcefield parameters with respect to given
>> >> >> residuum ?
>> >> >>
>> >> >> Thank you in advance for explanation of this very last technical
>> >>
>> >> detail
>> >>
>> >> >> !
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Marek
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> Dne Mon, 20 Apr 2009 14:27:45 +0200 Karl Kirschner
>> >> >>
>> >> >> <kkirsch_at_scai.fraunhofer.de> napsal/-a:
>> >> >> > Hello Marek,
>> >> >> >
>> >> >> > You should be able to model the "broken" glucose fine using
>> >> >>
>> >> >> Glycam_06.
>> >> >>
>> >> >> > Glycam_06 was parameterized using hydrocarbons, alcohols, and
>> >>
>> >> ethers
>> >>
>> >> >> > (plus a
>> >> >> > more limited number of nitrogen and RCO2- compounds; J. Comput
>> Chem
>> >> >>
>> >> >> 29,
>> >> >>
>> >> >> > 2008,
>> >> >> > 622). It was tested on a small molecule test suite and on
>> >> >>
>> >> >> carbohydrates.
>> >> >>
>> >> >> > Thus, Glycam_06 should work well for simulating the broken
>> glucose.
>> >> >> >
>> >> >> > You may be missing parameters for where the glucose is linked
>> to
>> >>
>> >> the
>> >>
>> >> >> > dendrimer. You could use parameters from either ff99 or gaff for
>> >>
>> >> the
>> >>
>> >> >> > missing
>> >> >> > parameters. Due to the flexibility and the number of highly
>> >>
>> >> rotatable
>> >>
>> >> >> > bonds
>> >> >> > of your system, it would be advantageous to test the resulting
>> >>
>> >> force
>> >>
>> >> >> > field
>> >> >> > against experiment or QM to validate your parameter choices.
>> >> >> >
>> >> >> > Cheers,
>> >> >> > Karl
>> >> >> >
>> >> >> > On Monday 20 April 2009 13:52, Marek Malý wrote:
>> >> >> >> Dear all, I have very last question to this topic.
>> >> >> >>
>> >> >> >> As I reported sooner I would like to simulate dendrimers
>> >> >> >> "decorated" with maltose.
>> >> >> >>
>> >> >> >> Unfortunately binding of maltose to terminal dendrimer amines
>> >> >> >> requires opening of one glucose ring and creating bond between
>> >> >> >> C1' and dendrimer terminal amine ( please see the attached
>> >>
>> >> picture ).
>> >>
>> >> >> >> In this case I assume that GLYCAM_06 forcefield could be
>> >> >> >> used only for parametrisation of the second ( unbroken )
>> glucose
>> >> >> >> ring and the broken one should be parametrised using GAFF ff.
>> >> >> >>
>> >> >> >> Am I right ?
>> >> >> >>
>> >> >> >>
>> >> >> >> Thanks in advance for answering of this my very last
>> >> >> >> question.
>> >> >> >>
>> >> >> >> Marek
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > AMBER mailing list
>> >> >> > AMBER_at_ambermd.org
>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >> >
>> >> >> > __________ Informace od NOD32 4021 (20090420) __________
>> >> >> >
>> >> >> > Tato zprava byla proverena antivirovym systemem NOD32.
>> >> >> > http://www.nod32.cz
> 

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