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: Mon Apr 20 2009 - 22:52:46 CDT

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
>
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