AMBER Archive (2008)

Subject: Re: AMBER: SMD RESTRAINTS

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Jun 12 2008 - 14:23:26 CDT

Dear Fatima,
That paper used the amber force fields and equations but NOT the amber
program as sold. In fact it used a home-made interface
between MM and Siesta for QM.

So, sander out-of-the-box cannot do what you ask for.

I was the lead author in the paper you mention, so we are taking the
code from that original program and putting it into amber to be able to
do 2-D pullings, but it is not yet done.

Adrian

fatima.chami_at_durham.ac.uk wrote:
> Quoting Adrian Roitberg <roitberg_at_qtp.ufl.edu>:
>
>> Fatima,
>> You cannot at this time do this.
>> We are working on code to do it as we speak. If you know enough fortran
>> you can go into src/sander/nmr.f and add this yourself
>> for your particular case. We want to make it more general.
>
>
> Thanks for replying
> according to this communication : "J.AM.CHEM.SOC.2005,127, 6940 "which is cited
> as ref 141 in Amber 9 manual .. the reaction coordinate was a distance difference
>
> what about using umbrella sampling ..would that be possible
>
> fatima
>
>> One option is to do a 2-D umbrella scan for the two distances.
>>
>> Cheers
>> Adrian
>>
>>
>> fatima.chami_at_durham.ac.uk wrote:
>>> Dear folks
>>>
>>> In a steered MD:
>>> the reaction coordinate is a difference between two distances ..how can i
>> set up
>>> such a restraint. Jar =1 does not allow more than one restraint
>>>
>>> any example of doing this
>>> best wishes
>>> Fatima
>>>
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>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>>
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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>>
>
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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