[AMBER] (no subject)

From: Steve Seibold <seibold.chemistry.msu.edu>
Date: Thu, 24 Jun 2010 14:14:19 -0400

Hi Jason
Thanks for your response/help.

>We would need to see your input file that you used. I'm guessing you did not specify ntwx (which is a number that specifies the interval of snapshots that is saved to the trajectory file)

>in your &cntrl namelist, which defaults to a value of 0. This means that coordinates are never written to the mdcrd, even though you may specify (-x test.mdcrd) on the command-line.

Here is my input file for SANDER (my command line does have -x file.mdcrd):


  ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 5, ntwx = 5000, ntwv = 0, ntwe = 50,
  ntwr = -5000,

  ntf = 1, ntb = 1,
  cut = 8.0, nsnb = 5,

  ibelly = 0, ntr = 0, nmropt = 0,

  imin = 0,
  nstlim = 10,
  nscm = 1000,
  t = 0.0, dt = 0.002,

  temp0 = 300.0, tempi = 300.0,
  ig = 71277,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,
  restraintmask= ':1-2495'
  restraint_wt =0,

  ntp = 0, pres0 = 1.0, comp = 44.6,
  taup = 0.2,

  ntc = 2, tol = 0.00001,
  lastrst = 8000000,


So, I am not sure why SANDER is not writing out the md trajectory files.


>How do you combine the trajectory files? Using cat to append one file to another? This would be bad

I am using ptraj to combine the trajectory files.
I am using AMBER8 trajectories which appear to be ok when visualized with VMD.

>I'm guessing it's just a different format that's triggering that error, and it can likely be ignored. You may consider just using the simple

>trajin mdcrd
>trajout new_mdcrd

I did "rewrite" amber8 trajectories using in AmberTools1.4 ptraj using:

trajin old.mdcrd
trajout new.mdcrd

I did this for two AMBER8 trajectory files called New.mdcrd and New1.mdcrd. However, as with other AMBER8 trajectories when I combined the two trajectories and used "rdparm" I got the same error: "Could not predict nubmer of frames...etc."

Could this have anything to do with how I compiled AMBER11 and its Toolset1.4??? It is not likely right since both packages passed their "TESTS"????

I really do appreciate your help. I just have a basic knowledge of this kind of stuff and am trying desperately to get AMBER11 up and running.

Thanks, Steve

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Received on Thu Jun 24 2010 - 11:30:03 PDT
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