AMBER Archive (2000)

Subject: (no subject)

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Fri Nov 17 2000 - 10:59:23 CST

Hello AMBERs -

Thank you all for the answers re: defining groups in AMBER - your
sugggestions worked, but I'm encountering now another problem: AMBER
inexplicably complains about and end-of-file in th einput, although it
has the two END statements, as required:

--------------------------------------------------------------------

Simmulated annealing
 &cntrl
  imin=0, irest=0, ntx=1,
  ntt=1, tempi=0., temp0=5000., tautp=2.0,
  ntb=0, ntr=1, scee=1.2,
  ntc=2, tol=0.00001, dt=0.002, ntf=2, ntcm=1,
  nstlim=25000, ntwx=500, ntpr=500,
 &end
Fix protein backbone:
100.0
FIND
* * M *
* H E *
* O E *
SEARCH
RES 101 107
END
Harmonically restrain sidechains:
10.0
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 1 7
END

[...snip...]

Harmonically restrain sidechains:
25.0
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 8
RES 28
RES 104
END
END

--------------------------------------------------------------------

And here's the output:

--------------------------------------------------------------------

          -------------------------------------------------------
          Amber 6 SANDER_CLASSIC Scripps/UCSF 1999
          -------------------------------------------------------

| Thu Nov 16 18:58:20 2000

  [-O]verwriting output

File Assignments:
|MDIN : sa2.in
|MDOUT: sa2.out
|INPCR: min.xyz
|PARM : /disk1/nachman/yeei.top
|RESTR: sa2.xyz
|REFC : min.xyz
|MDVEL: mdvel
|MDEN : mden
|MDCRD: sa2.crd
|MDINF: mdinfo

 Here is the input file:

Simmulated annealingB
 &cntrl
  imin=0, irest=0, ntx=1,
  ntt=1, tempi=0., temp0=5000., tautp=2.0,
  ntb=0, ntr=1, scee=1.2,
  ntc=2, tol=0.00001, dt=0.002, ntf=2, ntcm=1,
  nstlim=25000, ntwx=500, ntpr=500,
 &end
Fix protein backbone:
100.0
FIND
* * M *
* H E *
* O E *
SEARCH
RES 101 107
END
Harmonically restrain sidechains:
10.0
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 1 7
END

[...snip...]

Harmonically restrain sidechains:
25.0
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 8
RES 28
RES 104
END
END
-------------------------------------------------------------------------------

Simmulated annealing

| Reading &cntrl namelist w/ machine lib

[...snip...]

     GROUP 5 HAS HARMONIC CONSTRAINTS 25.00000
      ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = S RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = B RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = 3 RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = E RESIDUE TYPE = *

 GRP 5 RES 8 TO 8
 GRP 5 RES 28 TO 28
 GRP 5 RES 104 TO 104
      Number of atoms in this group = 38
    ----- READING GROUP 6; TITLE:
 END

     rfree: End of file on unit 5
-------------------------------------------------------------------

Thanks in advance,

Joseph

--------------------------------------------------------------------
Joseph Nachman Department of Biochemistry
nachman_at_hera.med.utoronto.ca University of Toronto
                                        Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
--------------------------------------------------------------------