Re: [AMBER] parameters for Lys-sugar P2N file

From: Urszula Uciechowska <>
Date: Mon, 26 Mar 2012 08:52:33 +0200

Dear Francois,

I prepared the p2n file for RED based on the Tutorial 3, however I am not quite sure how to specify in this case the part ...



REMARK Atoms to be kept in the final Tripos .mol2 file (to keep some compatibility with
REMARK other force field libraries already available in the AMBER force field topology database):
REMARK INTRA-MCC .... | | Keep
REMARK INTRA-MCC -... | | Keep

Could you suggest me something? Do I need specify anything else there?

Von: FyD []
Gesendet: Samstag, 24. März 2012 09:14
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for Lys-sugar

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

AMBER mailing list

AMBER mailing list

Received on Mon Mar 26 2012 - 00:00:03 PDT
Custom Search