AMBER Archive (2007)

Subject: AMBER: Surface

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Dec 06 2007 - 13:11:21 CST

Hi David,
I have asked before about studying DNA on a surface using amber7 before.
Unfortunately i did not get responses. Is it save to assume that this is
a difficult task. Or is the problem simply lack of interest in this
subject. your help is greatly appreciated.

Best wishes,
Taufik

David A. Case wrote:
> On Wed, Dec 05, 2007, fatima.chami_at_durham.ac.uk wrote:
>>
>> I started using the NMR approach. My restraint file contains
>>
>> &rst
>> iat= 8, 20, 21, 22,
>> r1=160.0,r2=165.8, r3=170.0, r4=171.0,
>> rk2=50, rk3=50,
>> ialtd=0, &end
>
> You probably need to have r4 much larger, if you want a 180 angle to be
> penalized by a significant amount. Try r4 at least at 180.
>
> You should plot your actual penalty function vs. angle to see visually what
> regions are allowed and disallowed, and by how much. As others have noticed,
> you get counter-intuitive results when r1 is very close to r2, or when r3 is
> very close to r4.
>
>> I selected iat with respect to sequence number in the Pdb file for the given
>> torsion angle
>>
>> my mdin file:
>>
>> &cntrl
>> imin = 1,
>> nmropt = 1,
>> pencut=-0.001
>> maxcyc = 500,
>> ncyc = 250,
>> ntb = 0,
>> igb = 0,
>> cut = 12
>> /
>> &wt type='REST', istep1=0,istep2=500,value1=0.1,
>> value2=1.0, /
>
> As you have seen, it won't work to use variable restraints with minimization:
> that only works for MD.
>
>> to check if my approach is working i run a minimization
>> at current torsional angle of 180.0 which is outside the restraint range
>
> Use the LISTIN=POUT command line to get detailed information on your
> restraints.
>
>
> ...hope this helps...dac
>
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