[AMBER] j-restrained peptide

From: Rossella Noschese <noschese.rossella.gmail.com>
Date: Wed, 3 Nov 2010 14:07:23 +0100

Hi, I'm a new user of amber(in my university we only have license for
amber7). I tried to run a restrained simulated annealing of a peptide.
1) I extracted my J(HNCalphaHalpha) values (J for ILE:8.06Hz; J for
VAL:7.56Hz) from my spectra and I added these restraints to my run.
First I used rjcoef A=6.4 B=-1.4 C=1.9 and rk2=rk3=32 and this was my
output:

  H VAL 2 -- HA VAL 2: 6.899 7.400 0.501 8.017 j
  H ILE 7 -- HA ILE 7: 6.900 7.900 1.000 32.000 j
                                       Total distance penalty: 0.850
                                       Total torsion penalty: 40.017
| RMS deviation from ideal bonds : 0.0166
| RMS deviation from ideal angles: 2.898

with a too large RMS deviation!!

Then I tried again changing rk2=rk3=10 and this was my output:
  H VAL 2 -- HA VAL 2: 7.601 7.600 0.001 0.000 j
  H ILE 7 -- HA ILE 7: 7.292 7.900 0.608 3.699 j
                                       Total distance penalty: 0.501
                                       Total torsion penalty: 3.699
| RMS deviation from ideal bonds : 0.0153
| RMS deviation from ideal angles: 2.578

which is better in the J value itself (for VAL 7.601) but still too large in
RMS deviation. Can you tell me if there's some parameter I can adjust to
have a good RMSd?

2) When I look at my pdb file my restrained dihedrals seem to be calculated
on teta instead of phi angles ( 3J=6.4cos2-1.4cos+1.9 with =-60) , am
I right? How can I have my dihedral from j value calculated on phi angles?

I attach my dyn.in and rst.tors
thanks for help
R.


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Received on Wed Nov 03 2010 - 06:30:04 PDT
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