Re: [AMBER] parameters for Lys-sugar

From: FyD <>
Date: Sat, 24 Mar 2012 09:14:17 +0100

Dear Lachele,

I think dihedral force field development is performed _after_ charge

In this case, one should (i) derive the charges and build the FF
library(ies) for the new molecular fragment(s), define the FF atom
types etc... (and may-be for models as well), and then (ii) perform MD
simulation to match experimental/QM data, and/or fit MM to a QM
profile. Indeed, non-bonded interactions are used during the dihedral
profile fit...

regards, Francois

> There is agreement in the group that the linkage position could be
> hard to model well. Of course, this depends on how well you need it
> modeled, but for the things we would normally do, we would take some
> time developing and validating, especially for something like this.
> On Fri, Mar 23, 2012 at 2:01 PM, Lachele Foley (Lists)
> <> wrote:
>> My concern isn't so much developing the charges so much as is finding
>> good parameters for the rest of the force field in the linkage
>> environment.  The anomeric center is complex to model all by itself.
>> If you add a positively charged group so close by, that's likely to
>> complicate things more.
>> For the charges, especially with the tight and complex charge
>> distribution you have there, I recommend an ensemble average.  If you
>> just use a few structures you might end up with charges that bias the
>> structure in some manner.  I think RED can be used for an ensemble of
>> structures.  Francois can help more with that.  We do all ours
>> in-house, of course.  But, the results should be equivalent.
>> Definitely validate whatever you decide to use.  Find experimental
>> j-couplings or something else that you can calculate from the
>> structure.  This is especially important in your situation.  If you
>> can't find any experimental values, then validate against appropriate
>> quantum structures.
>> On Fri, Mar 23, 2012 at 12:11 PM, FyD <> wrote:
>>> Urszula,
>>>> Thank you, this is a part of a peptide, attached is the whole
>>>> peptide structure ...
>>> So you might start from a dipeptide:
>>> R.E.D. Server can generate different fragemtnts automatically as well:
>>> regards, Francois
>>>> It's not really even a complete lysine, and the attachment is a bit
>>>> unusual.  The proximity of the ring oxygen, the anomeric oxygen and
>>>> the nitrogen -- all just one carbon removed from each other -- might
>>>> make good parameterization tricky.  I'll think about it a while and
>>>> ask around in the group.  I'll get back to you.
>>>> On Fri, Mar 23, 2012 at 11:06 AM, FyD
>>>> <> wrote:
>>>>> Dear Urszula,
>>>>>> I have a peptide with a sugar bound (beta-D-Glucose), and I would
>>>>>> like to run MD on that with a protein later. I am trying to find a
>>>>>> easy way to
>>>>>> generate the parameters for this part. I know that I could use a
>>>>>> RESP-A1A charge model for the entire new residue and scaling factors
>>>>>>  for 1-4 interactions.
>>>>>> However I have no idea how to start with that ...
>>>>>> I was wondering if there is any tutorial for that?
>>>>>> Could anyone suggest me something? I attached a mol2 file of the
>>>>>> residue with sugar bound.
>>>>> Does this Lys-Glc belongs to a peptide? if yes, this likely means you
>>>>> need a central fragment for this modified amino-acid. You might decide
>>>>> to start from a dipeptide; i.e. ACE-AA*-NME; AA* is your modified
>>>>> amin-acid; i.e. Lys-beta-D-Glucose.
>>>>> See
>>>>> or, you might decide to split your molecules into two parts; a glyco
>>>>> part and a AA part...
>>>>> regards, Francois

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Received on Sat Mar 24 2012 - 01:30:03 PDT
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