I think Alex is right. my student suggests using this kind of syntax instead:
Try writing :2.P, :2.C1',C2',C3',C4',O4', :3.P, :3.C1',C2',C3',C4',O4'
On Mon, Aug 4, 2008 at 12:58 PM, Alex Spasic <als254.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.P,
>>> com(:2.C1',:2.C2',:2.C3',:2.C4',:2.O4'),:3.P,com(:3.C1',:3.C2',:3.C3',:3.C4',:3.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
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Aug 06 2008 - 06:07:25 PDT
