AMBER Archive (2002)

Subject: problem in sander

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 10 2002 - 21:11:06 CDT

Hi amber users,

1. I have amber7 compiled and running on an origin cluster SGI Origin2000
(O2K)
2. I am trying to do a minimization for a protein (total number of
residues 2051 plus 818 crystallografic waters, meaning a total of about
35000 atoms). I am imposing restraints on all the heavy atoms and only
want to fix the position of the hydrogens (the input file is attached at
the bottom of this message).
3. If I use a cutoff value of 100A I get the following error message:

| Flags: SGIFFT MEM_ALLOC HAS_FTN_ERFC
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file being parsed.
|Version = 1.000 Date = 10/07/02 Time = 12:55:44
 NATOM = 34759 NTYPES = 16 NBONH = 18344 MBONA = 16779
 NTHETH = 36099 MTHETA = 22715 NPHIH = 68670 MPHIA = 41972
 NHPARM = 0 NPARM = 0 NNB = 181415 NRES = 2869
 NBONA = 16779 NTHETA = 22715 NPHIA = 41972 NUMBND = 43
 NUMANG = 88 NPTRA = 40 NATYP = 29 NPHB = 1
 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 Failed to allocate memory for ipairs: 604076661

What is the best thing to do in this case?

4. If I reduce the cutoff value to 25A then I get at the prompter the
following error message:

MPI: MPI_COMM_WORLD rank 3 has terminated without calling MPI_Finalize()
MPI: aborting job

and in the output file
 Exceeding lastist in get_istack
   lastist = 2000000
   top_stk= 1791568
   isize = 221284
   request= 2012852
  Increase lastist in the &cntrl namelist

I am running this job on 4 processors however only one seems to be
failing. Any idea what is causing this?

About the lastist: In sizes.h it is advised to override the MAX_ISTACK
value by defining indeed lastist in the &cntrl list. What is the limiting
value that one can use for lastist?

4. Regarding the restraints, I noticed that sander does not seem to be
able to make a difference between atoms defined like:
 * CD * *
and atoms of the following type:
 * CD1 * *

Is there something wrong in my definition?

Thank you in advance,
Ioana

******************************input file*******************
minimization to fix up hydrogen positions
 &cntrl
  cut = 25.0,
  ntx = 1, irest = 0
  ntr = 1,
  ntb = 0,
  igb = 0,
  imin = 1, maxcyc = 5000, ncyc = 2000, ntmin = 1, drms=0.05,
  scee=1.2, ntpr = 10,
 &end
Restrain the 7AHL heavy atoms
5000.0
FIND
 * N * *
 * NZ * *
 * ND1 * *
 * ND2 * *
 * NE * *
 * NE1 * *
 * NE2 * *
 * NH1 * *
 * NH2 * *
SEARCH RES 1 2051
END
Restrain the 7AHL heavy atoms II
5000.0
FIND
 * CA * *
 * CB * *
 * CD * *
 * CD1 * *
 * CD2 * *
 * CE * *
 * CE1 * *
 * CE2 * *
 * CE3 * *
SEARCH
RES 1 2051
END
Restrain the 7AHL heavy atoms III
5000.0
FIND
 * CG * *
 * CG1 * *
 * CG2 * *
 * CH2 * *
 * CZ * *
 * CZ2 * *
 * CZ3 * *
 * C * *
 * O * *
SEARCH
RES 1 2051
END
Restrain the 7AHL heavy atoms IV
5000.0
FIND
 * OD1 * *
 * OD2 * *
 * OG * *
 * OG1 * *
 * OH * *
 * OXT * *
 * OE1 * *
 * OE2 * *
 * SD * *
SEARCH
RES 1 2051
END
END
**********************************EOF*************************