AMBER Archive (2005)

Subject: AMBER: Format of atom specifiication after FIND

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Tue Aug 16 2005 - 14:02:55 CDT

Hello Ambers -

I'm trying to run an MD with ibelly, where I allow certain side-chains to
move. The prgram seems to choke onthe side chain definition after FIND:

    ----- READING GROUP 1; TITLE:
 Fix the structure except for peptide residues and and sc of Arg62 and its
 GRP 1 RES 106 TO 110
      Number of atoms in this group = 89
    ----- READING GROUP 2; TITLE:
 FIND

     rfree: Error decoding variable 2 2 from:
* *

Obviously something is wrong withthe format, but I couldn't find the
right one. Does anyone has any idea?

Thanks in advance,

Joseph

Here is my input file:

-------------------------------------------------------------------
Mutant ThrEF1Trp Src SH2 domain with pYEEI
 &cntrl
  imin=0, nmropt=1, irest=0, ntx=1, idiel=0,
  ntt=1, temp0=3000., tautp=1.0, ibelly=1,
  ntb=0, ntr=1, scee=1.2, cut=20.0, nsnb=100000,
  ntc=2, tol=0.0050, dt=0.0005, ntf=2, ntcm=1,
  nstlim=80000, ntwx=100, ntwxm=0, ntpr=250,
 &end
 &wt
  type='TEMP0', istep1=0, istep2=20000, value1=0., value2=1000.,
 &end
 &wt
  type='TEMP0', istep1=20000, istep2=40000, value1=1000., value2=2000.,
 &end
 &wt
  type='TEMP0', istep1=40000, istep2=60000, value1=2000., value2=3000.,
 &end
 &wt
  type='TEMP0', istep1=60000, istep2=80000, value1=3000., value2=3000.,
 &end
 &wt
  type='END',
 &end
DISANG=dummy

Medium restraints on pTyr:
25.0
SEARCH
RES 106
END
END
Fix the structure except for peptide residues and and sc of Arg62 and its neighbours:
SEARCH
RES 106 110
END
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 59 62
RES 68 69
END
END 

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

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