AMBER Archive (2008)

Subject: Re: AMBER: Problem with setting the NMR restraints

From: Alex Spasic (als254_at_cornell.edu)
Date: Mon Aug 04 2008 - 11:58:17 CDT

Thank you David. However I believe that starting from Amber 10 one
should be able to use atoms groups in angles and torsions. This is
written in the Amber 10 manual on page 169 and the example is given on
the page 170. Perhaps Matthew can give a definite answer.
Btw. I have tried using the old notation in Amber 10 as well (without
the new 'restraint' keyword) but it also doesn't work.

David A. Case wrote:
> On Mon, Aug 04, 2008, Alex Spasic wrote:
>
>> I am trying to run a simulation of a small single chain DNA fragment
>> using Amber 10 while holding fixed the torsion angle formed by the:
>>
>> (phosphate)i-(center of mass of sugar)i-(phosphate)i+1-(center of mass
>> of sugar)i+1
>>
>> The restraint is defined by the following lines:
>>
>> # psps restraint
>> &rst restraint = "torsion[:2_at_P,
>> com(:2_at_C1',:2_at_C2',:2_at_C3',:2_at_C4',:2_at_O4'),:3_at_P,com(:3_at_C1',:3_at_C2',:3_at_C3',:3_at_C4',:3_at_O4')]",
>> r1 = -180, r2 = -150.0, r3 = -150.0, r4 = -120.0,
>> rk2 = 30.0, rk3 = 30.0
>> /
>>
>>
>
> As I remember (and from browsing briefly through he code) only distance
> restraints can use the center of mass idea. It looks like the new format for
> restraint input doesn't enforce this restriction. Matthew Seetin should look
> at this and confirm (or not), but my intial guess is that you can't do what
> you are trying here.
>
> ...dac
>
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