AMBER Archive (2009)

Subject: [AMBER] implicit_run_error

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Thu Nov 19 2009 - 12:37:21 CST

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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