AMBER Archive (2008)

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

From: Alex Spasic (als254_at_cornell.edu)
Date: Mon Aug 04 2008 - 14:35:20 CDT

Carlos thank you for your suggestion. Unfortunately this doesn't work
for me. I'm getting the message that the input is not formatted
correctly. I think that ambmask format has to be :(residue#)@(atom name).

Carlos Simmerling wrote:
> 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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