----- Forwarded message from dch1fc.smtphost.dur.ac.uk -----
Date: Wed, 5 Dec 2007 18:10:20 +0000
From: dch1fc.smtphost.dur.ac.uk
Reply-To: dch1fc.smtphost.dur.ac.uk
Subject: Re: AMBER: leap restrainTorsion
To: amber.scripps.edu
Dear David,
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
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, /
&wt type='END' /
LISTOUT=POUT
DISANG=disang.rst
to check if my approach is working i run a minimization
at current torsional angle of 180.0 which is outside the restraint range
the output looks fine and the structure did not change
is it possible to restraint to 170.0 (target value)
the output shows: 'what is LINMIN'
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -1.8637E+02 7.0025E-01 2.9346E+00 S1 30
BOND = 1.6594 ANGLE = 19.9446 DIHED = 15.1397
VDWAALS = 16.5743 EEL = -279.9287 HBOND = 0.0000
1-4 VDW = 13.2861 1-4 EEL = 26.7777 RESTRAINT = 0.1801
EAMBER = -186.5470
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.180
===============================================================================
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -1.8637E+02 1.4297E-01 5.4922E-01 N1 22
BOND = 1.6609 ANGLE = 20.0324 DIHED = 15.1401
VDWAALS = 16.4447 EEL = -279.9129 HBOND = 0.0000
1-4 VDW = 13.2780 1-4 EEL = 26.7917 RESTRAINT = 0.1993
EAMBER = -186.5651
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.199
===============================================================================
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
363 -1.8637E+02 1.1437E-01 4.9341E-01 C3 8
BOND = 1.6507 ANGLE = 20.0529 DIHED = 15.1554
VDWAALS = 16.3544 EEL = -279.8437 HBOND = 0.0000
1-4 VDW = 13.2835 1-4 EEL = 26.7889 RESTRAINT = 0.1900
EAMBER = -186.5578
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.190
===============================================================================
------------------------------------------------------------------------------
Final Restraint Analysis for coords: edicol6_vac_min.rst
Restraints, deviations, and energy contributions: pencut = 0.00
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
C4 UNK 1 -- N2 UNK 1: 178.800 170.000 8.800 0.190 t
Total torsion penalty: 0.190
| RMS deviation from ideal bonds : 0.0096
| RMS deviation from ideal angles: 3.783
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
MANY THANKS
FATIMA
Quoting "David A. Case" <case.scripps.edu>:
>
> On Wed, Dec 05, 2007, fatima.chami.durham.ac.uk wrote:
> >
> > I have used the restrainTorsion command in Leap to generate topology files
> and
> > run minimization with sander but it did not work cause sander does not
> read
> > restrains from topology file.
> >
> > I am aware of NMR refinement but i taught that the easiest way is via Leap
>
> No, the "easiest way" has to be the one that works :-) You should plan on
> using the NMR restraint approach. [Others can chime in here if I am missing
> some other option.]
>
> ...dac
>
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Received on Sun Dec 09 2007 - 06:07:12 PST
