AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Aug 04 2008 - 13:28:36 CDT

I think Alex is right. my student suggests using this kind of syntax instead:

Try writing :2_at_P, :2_at_C1',C2',C3',C4',O4', :3_at_P, :3_at_C1',C2',C3',C4',O4'

On Mon, Aug 4, 2008 at 12:58 PM, Alex Spasic <als254_at_cornell.edu> wrote:
> 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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>
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-- 
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