[AMBER] Could not read velocities from amin.crd

From: Ashutosh Shandilya <izerokelvin.gmail.com>
Date: Sat, 27 Nov 2010 12:20:13 +0530

I minimized the dna first restarined and then free minimization.When I
started heating it says could not read velocities from the crd file.The crd
file is with the attachment.

The input file for restrained minimization is:
First Minimization
&cntrl
   imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1,
   cut=9.0, nsnb=10, ntr=1, maxcyc=1000, ncyc=500, ntmin=1,
        /
Group input for DNA restraints: 25 kcal/mol.
 25.0
RES 1 24
END
END

Input for free minimization:

Second Minimization, No restraints
&cntrl
   imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1,
   cut=9.0, nsnb=10, ntr=0, maxcyc=1000, ncyc=500, ntmin=1,
        /
Input for heating and equilibration

First heating/equilibration run
&cntrl
    imin=0,rest=1, ntx=5, ntpr=5000, ntwr=5000,
    ntf=2, ntc=2,
    ntb=2, ntp=1, taup=5.0,
    nstlim=500000, dt=0.002,
        tempi=0.0, temp0=298.0,
    cut=9.0,
    ntt=3, gamma_ln=1.0
 /

Regards

Shandilya Ashutosh


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Received on Fri Nov 26 2010 - 23:00:02 PST
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