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*************************
Received on Thu Oct 10 2002 - 19:11:06 PDT
