AMBER Archive (2007)

Subject: Fwd: Re: AMBER: leap restrainTorsion

From: fatima.chami_at_durham.ac.uk
Date: Wed Dec 05 2007 - 12:45:24 CST

----- Forwarded message from dch1fc_at_smtphost.dur.ac.uk -----
    Date: Wed, 5 Dec 2007 18:10:20 +0000
    From: dch1fc_at_smtphost.dur.ac.uk
Reply-To: dch1fc_at_smtphost.dur.ac.uk
 Subject: Re: AMBER: leap restrainTorsion
      To: amber_at_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_at_scripps.edu>:

>
> On Wed, Dec 05, 2007, fatima.chami_at_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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