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.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.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.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.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
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 12:22:58 PDT
