Dear Amber !
I am trying to do implicit minimization and equilibration for DNA .
The minimization part was performed ,
the script as below
&cntrl
imin=1,
maxcyc=500,
ncyc=250,
cut=12.0,
igb=2,
saltcon=0.2,
gbsa=1,
intdiel=1.0,
extdiel=78.5,
ntpr=10,
ntx=1,
ntb=0,
ntr=1,
/
keep all atoms restrained
5.0
RES 1 80
END
END
---------------------------
when i do the equilibration the run is not performed it gave the error 5. REFERENCE ATOM COORDINATES
| INFO: Old style inpcrd file read
----- READING GROUP 1; TITLE:
rfree: Error decoding variable 1 3 from:
kepp
the input file I gave is
this indicates that your input contains
incorrect information
field 1 was supposed to
------------------------
the input file I gave is
&cntrl
imin=0,
ntc=2,
ntf=2,
cut=12.0,
igb=2,
saltcon=0.2,
gbsa=1,
intdiel=1.0,
extdiel=78.5,
ntpr=50,
nstlim=10000,
dt=0.002,
ntt=1,
tempi=0,
temp0=300,
tautp=1.0,
ntx=1,
irest=0,
ntb=0,
nscm=1000,
ntr=1
/
kepp all atom restrained
1.0
RES 1 80
END
END
----------------------
could any one help me, where i have done mistake !
regards
balaji
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Received on Thu Nov 19 2009 - 11:00:02 PST
