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 Malư 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 Malư 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
> >
> > _______________________________________________
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> > 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
--
------------------------------------
Karl N. Kirschner, Ph.D.
Fraunhofer-Institute for Algorithms
and Scientific Computing - SCAI
Department of Simulation Engineering
Schloss Birlinghoven
53754 Sankt Augustin, Germany
Tel: +49 (0) 2241-14-2052
Fax: +49 (0) 2241-14-1328
------------------------------------
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Received on Wed May 20 2009 - 11:56:48 PDT
