AMBER Archive (2008)

Subject: RE: AMBER: error in reading namelist cntrl

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 30 2008 - 15:26:38 CDT

Hi Maria,

You need to have the &cntrl in column 2. It looks like you have it in column
1. The same is true for &end. Although you are probably better using a /
which should work on more machines. I.e. your input file should be:

molecular dynamics run
 &cntrl
  imin=0, nmropt=1, ntx=1, irest=0, ntpr=100,
  iwrap=1, ntwx=100, ntr=1, nstlim=50000,
  dt=0.002, ntt=1, temp0=298.15, tempi=0.0,
  ig=71277, tautp=1.0, ntp=1, pres0=1.0,
  comp=44.6, taup=1.0, npscal=1.0,
  ntc=2, tol=0.00005, ntf=2, ntb=2,
  dielc=1.0, cut=8.0, nsnb=50.0
 /
 &wt
  type='TEMP0', istep1=0, istep2=25000,
  value1=0.0, value2=298.15,
 /
 &wt
  type='TEMP0', istep1=25000, istep2=50000,
  value1=298.15, value2=298.15,
 /
 &wt
   type='END'
 /
restain DNA and labels
20.0
RES 1 25
END
END

I am amazed that AMBER 8 worked while AMBER 10 didn't, I don't think much
has changed in the input file reading, more likely you compiled amber 10
with a different compiler than amber 8 and it is more picky about sticking
to the standard.

If this doesn't help then we'll need to see your input file.

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Maria Frushicheva
> Sent: Monday, June 30, 2008 1:03 PM
> To: amber_at_scripps.edu; amber_at_scripps.edu
> Subject: AMBER: error in reading namelist cntrl
>
> Dear Miss or Mister,
>
> I'm using Amber 10. And I've tried to run an equilibration process.
> Previously I used Amber 8, so I've decided to used the old input file.
> Amber8 is working with this input file, but Amber 10 give me the following
> mistake: error in reading namelist cntrl. Below is my output file. And
> I've read the Amber10 manual and check all spell in my input file. I still
> don't know what is wrong. May you help me to solve this question.
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | Run on 06/27/2008 at 16:05:53
> [-O]verwriting output
>
> File Assignments:
> | MDIN: in.eq1
> | MDOUT: sim3_7R.outmd.eq1
> |INPCRD: sim3_7R.resmd.min
> | PARM: sim3_7R.tpmv
> |RESTRT: sim3_7R.resmd.eq1
> | REFC: sim3_7R.res.min
> | MDVEL: junk1.eq1
> | MDEN: junk2.eq1
> | MDCRD: sim3_7R.coord.eq1
> |MDINFO: junk.eq1
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
> |
>
> Here is the input file:
>
> molecular dynamics run
> &cntrl
> imin=0, nmropt=1, ntx=1, irest=0, ntpr=100,
> iwrap=1, ntwx=100, ntr=1, nstlim=50000,
> dt=0.002, ntt=1, temp0=298.15, tempi=0.0,
> ig=71277, tautp=1.0, ntp=1, pres0=1.0,
> comp=44.6, taup=1.0, npscal=1.0,
> ntc=2, tol=0.00005, ntf=2, ntb=2,
> dielc=1.0, cut=8.0, nsnb=50.0
> &end
>
>
> &wt
> type='TEMP0', istep1=0, istep2=25000,
> value1=0.0, value2=298.15,
> &end
>
> &wt
> type='TEMP0', istep1=25000, istep2=50000,
> value1=298.15, value2=298.15,
> &end
>
> &wt
> type='END'
> &end
>
> restain DNA and labels
> 20.0
> RES 1 25
> END
> END
>
> error in reading namelist cntrl
>
> Thank you for your assistance,
> Maria
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