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.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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Received on Tue Aug 16 2005 - 20:53:02 PDT
