[AMBER] SANDER BOMB

From: Xioling Chuang <xioling_c.hotmail.com>
Date: Thu, 9 Jun 2011 16:41:29 +0200

Dear All,
 
I am using amber9 to run MD of a small DNA duplex solvated in POL3 water model.
First, I minimized WAT and counterions without any problem. Then, I run MD with restrained on DNA and I got an error message.
Input file is
=============
 20ps MD with restrained on DNA
 &cntrl
  ntb = 2, ntp = 1,
  ntc = 2, ntf = 2,
  ntt = 3, cut = 9.0,
  ipol = 1,
  temp0 = 300.0, ntr = 1,
  gamma_ln = 1.0,
  nstlim = 20000, dt = 0.001,
  ntpr = 1, ntwx = 1000, ntwr = 1
 /
Fix DNA
1000.0
RES 1 8
END
END
=============
 
Here I tried to set ntpr=1 to see what happen. Please see attached file for the output.
Any suggestion, please?
 
Regards,
Xioling
                                                

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Received on Thu Jun 09 2011 - 08:00:03 PDT
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