[AMBER] unable to run minimizations after new installation of amber11

From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch>
Date: Thu, 6 Jun 2013 18:59:25 +0000

Dear all,

We recently made a new installation of amber11 from scratch with ambertools1.5 incl the bugfix.all. Although most of the tests I've run so far work well (xleap and MD production with pmemd), I have this problem with all the minimization/equilibration tests I've run with pmemd. This is 21-nt RNAs I'm running, with explicit solvent.

I've tried different crd and top files, all of which would work well in the past using the same scripts im using now, but each of them give me this error since the new installation: 
----
At line 109 of file inpcrd_dat.f90 (unit = 9, file = 'TSL2_1N8R.wat.min1')
Fortran runtime error: End of file
  Unit    9 Error on OPEN: TSL2_1N8R.wat.min2
STOP PMEMD Terminated Abnormally!
----
then I get this fort.16 file. The file TSL2_1N8R.wat.min1 is in blank. the .out files do not give any clue as to why pmemd stopped, and I really dont know what this means. this is what I run:
min1.in:
Min of just waters
 &cntrl
        imin=1, maxcyc=5000, ncyc=100, drms=0.5, ibelly=1,
        ntb=1,
 &end
Atoms that are going to move in the minimization
RES 22 7000
END
END
min2.in:
Min of all
 &cntrl
        imin=1, maxcyc=5000, ncyc=50, drms=0.2,
        ntb=1,
 &end
md1.in:
 &cntrl
  ntf=2, ntb=2,
  iwrap=1,
  ntr=1,
  nstlim=20000,dt=0.001,
  temp0=100, ntt=1,
  ntp=1,
  ntc=2,
 &end
Restrain DNA,counterions
100.0
RES 1 69
END
END
etc etc
I've tried to find a similar error on previous mails from the amber list, but in all the cases I found, it came together with other error messages.
http://archive.ambermd.org/201204/0027.html
http://archive.ambermd.org/201108/0198.html
I apologise because this is probably something very obvious, and I know it looks like a problem with my files, but I'm lost because it's exactly the same scripts, and the same topologies and coordinates I was running before (and not just for one molecule, I've tried three).
Thanks very much in advance for any ideas.
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel:  +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 06 2013 - 12:30:03 PDT
Custom Search