AMBER Archive (2008)

Subject: Re: AMBER: about glycam06

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Wed Apr 30 2008 - 16:47:32 CDT

> hi, thanks very much!
> could you explain more about the electronic parameters to me?

These are the partial atomic charges on atoms. I simply called them
parameters b/c they are inputs into the force field equation.

> sorry to bother you! If I don't have the periodic bondary
> condition, do you know which method and parameters I can use?

This is not quite clear. Non-periodic boundary conditions could be gas
phase, spherical droplet or implicit solvent. Also what do you mean by
which method and parameters to use?

>
> And if I want to see how the H-bond break during my simulation, is
> it fine to only use these two methods? Or I can combine the H-bond
> parameter in the previous force filed with glycam06?

Please let me know which two methods you have in mind. Given that the
h-bond parameters were not included in the development of glycam06, you
might get spurious results. You can monitor hydrogen bond formation over
the course of your simulation with either carnal or ptraj.

>
> Thanks a lot!
>
> Ying
>
> On Wed Apr 30 13:26:44 EDT 2008, "Austin B. Yongye"
> <ayongye_at_chem.uga.edu> wrote:
>
>> You are right. There are no 12-10 h-bond terms in Glycam06. AMBER
>> got rid
>> of these. Nonetheless, the electrostatic and vdW parameters in
>> Glycam06
>> are sufficient to handle h-bonding.
>> Austin-
>>
>>> Hi, Dear Amber users,
>>> I implement Glycam06 into another MD code to perform simulation.
>>> But I can not find Hydrogen bond terms in Glycam06.dat. Could
>>> anybody tell me how can I define the Hydrogen bond parameters
>>> when
>>> I use Glycam06 forcefield?
>>>
>>> Thanks very luch!
>>>
>>> Ying
>>> --
>>> WANG,YING
>>>
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>
>
>
> --
> WANG,YING
> Mechanical and Aerospace Engineering
> University of Florida
> Office: NEB 139
> TEL: 001-352-846-3030
>
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Austin B. Yongye, Ph.D.
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263

"...then, we learn better in a free spirit of curiosity, than under fear
and compulsion..." -St. Augustine of Hippo
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