AMBER Archive (2009)

Subject: Re: [AMBER] RDC and alignment tensor

From: Eliana Asciutto (ekasciut_at_gmail.com)
Date: Mon Oct 19 2009 - 11:50:31 CDT

Hi Tom,
Thanks for your detailed response. I tried it but in the first minimization
step I have a 'Nan" value for the RMS. Amber suggests trying without shake.
I also tried decreasing the dwt value, but I got the same error.

Here is my input file:

&cntrl
        imin=1, maxcyc=1000,ncyc=1000,
        ntc=2,ntf=2,nscm=500,
        ntb=1, cut=10,
        ntpr=10,
        nmropt=1,
/
  &wt type='END' /
LISTOUT=POUT
DIPOLE=RST.dip
END

RST.dip file:

&align
   ndip=47, gigj = 47*-3.163, dwt=47*0.05,
   freezemol=.true.,num_datasets=1,
   dataset=1
   id(1)=76, jd(1)=77, dobsl(1)=0.2, dobsu(1)=20.2,
   id(2)=111, jd(2)=2, dobsl(2)=-7.5, dobsu(2)=12.5,
   id(3)=199, jd(3)=200, dobsl(3)=-18.9, dobsu(3)=1.1,
   id(4)=244, jd(4)=245, dobsl(4)= -23.4, dobsu(4)=3.4,
   id(5)=437, jd(5)=438, dobsl(5)=3.5, dobsu(5)=23.5,
   id(6)=470, jd(6)=471, dobsl(6)=-35.2, dobsu(6)=-15.2,
   id(7)=481, jd(7)=482, dobsl(7)=3.4, dobsu(7)=23.4,
   id(8)=642, jd(8)=643, dobsl(8)=7.3, dobsu(8)=27.3,
   id(9)=657, jd(9)=658, dobsl(9)=-9.5, dobsu(9)=10.5,
   id(10)=668, jd(10)=669, dobsl(10)=3.4, dobsu(10)=23.4,
   id(11)=724, jd(11)=725, dobsl(11)=-12.6, dobsu(11)=7.4,
   id(12)=853, jd(12)=854, dobsl(12)=4.2, dobsu(12)=24.2,
   id(13)=860, jd(13)=861, dobsl(13)=4.6, dobsu(13)=24.6,
   id(14)=920, jd(14)=921, dobsl(14)=-12.6, dobsu(14)=7.4,
   id(15)=944, jd(15)=945, dobsl(15)=2.0, dobsu(15)=22.0,
..
..
..

And the output:

 NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -1.5672E+05 NaN 0.0000E+00 FE 1

 BOND = 1275.0642 ANGLE = 3721.6281 DIHED =
4155.6987
 VDWAALS = 13695.9798 EEL = -196533.7532 HBOND =
 0.0000
 1-4 VDW = 1425.1349 1-4 EEL = 15534.2111 RESTRAINT =
 3.1587
 EAMBER = -156726.0363
 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
 Energy (this step): Align= 3.159 CSA= 0.000
          Alignment tensor: 0.000 0.000 0.000
                                0.000 0.000 0.000
                                0.000 0.000 0.000
===============================================================================

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
  *** Especially for minimization, try ntc=1 (no shake)

Regards,

Eliana

On Fri, Oct 16, 2009 at 4:45 PM, Thomas Cheatham III <tec3_at_utah.edu> wrote:

>
> > We are trying to apply RDC constraints to our system.
> > We used PALES to generate preliminary alignment tensor components. In the
> > PALES output file, it is reported the 'Data Saupe Matrix' and the 'Data
> > irreducible representation'.
> > Which representation should I use for the initial values of the cartesian
> > components of the alignment tensor (s11,s12,s13,s22,s23) ?
> > And also, do I need to multiply by 10**5 as the manual suggests?
>
> Hopefully I have this right, otherwise DAC can correct me :-)
>
> I do not know how to do the conversion's yet from PALES or X-Plor, but I
> can tell you how to get an initial alignment tensor that works in MD
> with AMBER... In the RDC file, in the &align namelist, set
> freezemol=.true., i.e.
>
> &align
> ndip=51, dcut = -1.0, gigj = 51*7.84665, dwt = 51*0.05,
> s11 = -16.662, s22 = -14.584, s12 = -21.116, s13 = 54.695, s23 = -38.250,
> freezemol=.true.,
>
> id(1)=12, jd(1)=13, dobsu(1)= 22.60, dobsl(1)= 22.60,
> id(2)=9, jd(2)=10, dobsu(2)= -11.60, dobsl(2)= -11.60,
> ...
>
> You can have any initial sXY values. Note that the DWT values have to
> be fairly low; when we used higher values, the restraints were too
> strong leading to high frequencies in MD and shake failure...
>
> Then perform a minimization (it will usually converge in fewer than 1000
> steps):
>
> &cntrl
> imin=1, maxcyc=1000, ncyc=1000,
> ntc=2, ntf=2, nscm=500,
> ntb=1,
> cut=9.0,
> ntpr=10,
> nmropt=1,
> /
> &wt TYPE='END',
> /
> DISANG=noe-restraints.in
> DIPOLE=rdc-restraints.dip
>
> This will converge to the "AMBER" definitions of the alignment tensor
> (which depend on the orientation of the molecule). These can be extracted
> from the mdout file with the following Perl script. Note that you will
> want to remove freezemol=.true. from "rdc-restraints.dip" during the MD!
> At the end of each MD run, I run the Perl script again to get the tensors
> for the next round of MD...
>
> #!perl
>
> while ( <> ) {
>
> $text = $_;
>
> if ( /Alignment tensor/ ) {
>
> $_ = $text;
> ($s11, $s12, $s13) = / * Alignment tensor: (.*\d*\.\d*)
> *(.*\d*\.\d*) *(.*\d*\.\d*) */;
> $_ = <>;
> ($s21, $s22, $s23) = / * (.*\d*\.\d*) *(.*\d*\.\d*) *(.*\d*\.\d*)
> */;
> $_ = <>;
> ($s31, $s32, $s33) = / * (.*\d*\.\d*) *(.*\d*\.\d*) *(.*\d*\.\d*)
> */;
>
> }
> }
>
> printf(" Final alignment tensor found: \n");
> printf(" %7.3f %7.3f %7.3f\n", $s11, $s12, $s13);
> printf(" %7.3f %7.3f %7.3f\n", $s21, $s22, $s23);
> printf(" %7.3f %7.3f %7.3f\n\n", $s31, $s32, $s33);
>
> rename "rdc-restraints.dip", "rdc-restraints.dip.bak";
>
> open(IN, "rdc-restraints.dip.bak") || die;
> open(OUT, "> rdc-restraints.dip") || die;
>
> while (<IN>) {
> $text = $_;
>
> if ( /s11 =/ ) {
> printf(OUT " s11 = %7.3f, s22 = %7.3f, s12 = %7.3f, s13 = %7.3f,
> s23 = %7.3f,\n",
> $s11, $s22, $s12, $s13, $s23);
> } else {
> print OUT $text;
> }
> }
>
> close(IN);
> close(OUT);
>
> --------------
>
> Hope this helps --tec3
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Eliana K. Asciutto, Ph.D.
Department of Chemistry & Biochemistry
Center for Computational Sciences
Duquesne University
308 Mellon Hall
600 Forbes Avenue
Pittsburgh, PA 15282
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