Dear Amber-Users:
I am trying to calculate free energy change for moving atom
#3295 towards atom #2967 keeping the atom #13906 at a fixed position in a
protein. I use the cutoff = 15. in future I want to use larger cutoff. My
input file is given below. When I run Gibbs i get the following error. I am
using AMBER version 5. Can anyone please let me know what changes I need to
make and compile the code so that I can use larger cutoff ie RESNBA. Please
be elaborate.
In addition, if anyone finds anything wrong with my input file please point
that out.
Thanking you in advance,
Asif
------------------
error --- last part of the output file.
------------------
|
|
|
READING MOLECULAR TOPOLOGY FILE (PPARM)
--------------------
DYNAMIC MEMORY
ALLOCATED USED
| INTEGER: 7000000 857097
| REAL: 7000000 1448407
| CHARACTER: 291666 87110
| AVAILABLE INTEGER WORDS x 1 N-B PAIRS/WORD = 6142903 MAXIMUM N-B PAIRS
|
|
|
-------------------
Solute/solvent pointers:
IPTSOL= 913 NATRCM=14208
IPTRES= 0 IPTATM= 0
NSPSOL= 0 NSPSTR= 0
NSOLUT=14208 NATOM =14208
| Total accumulated time: 23.69 (seconds) / 0.01 (hours)
%GIBBS-I-NEWRUN, Begining NRUN = 1
ERROR from RESNBA: Number of non-bonded pairs exceeds the maximum
allowable ( 1535725). Increase integer storage.
Shared memory implementation: blew scratch array space in resnba
for thread 2 with the total pairs exceeding the value reported above.
The actual total effective number of allowable pairs is 6142900.
-----------------------------
Here is my input file:
---------------------------------
Title
&cntrl irest=0, ibelly=1,
ntx=1, ntxo=1, ig=150899, tempi=300.0,
ntb=0,
nrun=51, ntt=1, temp0=300.0, dtemp=00.0, tautp=0.2,
ndfmin = 0, ntcm = 1, nscm = 0,
nstlim = 2000, init = 3, t=0.0, dt=0.001,
ntc=2, tol=0.0005, ncorc=1, itimth = 0, ibigm = 1, ishkfl=1, jfastw = 0,
ntf=1, ntid=0, ntnb=1, nsnb=1000, idiel=1, intprt=5,
cut=15.0, cut2nd=0.0, scnb = 2.0, scee = 1.2, dielc = 1.0,
ntpr=100, ntwx=1000, ntwv=-1, ntwe=10, ioutfm=0, isande=1, iperat=1,
ntwxm = 999999, ntwvm = 999999, ntwem = 999999,
ntr=1, ntrx=1, intr=1, iatcmp=1, ntatdp=-1,
almda = 1.0, almdel = 0.02, isldyn = -3, idifrg = 0,
nstmeq = 1000, nstmul = 1000, ndmpmc = 1, idwide = 0,
&end
set restraints on evaporating waters for glh
1.50
RES 867 867 869 869 872 875 881 881 883 884 895 895
END
END
designating the belly for molecular dynamics
RES 1 6 9 10 22 46 92 104 106 108 111 114 116 127
RES 170 200 206 247 249 250 284 287
RES 296
RES 298 299 312 313 315 328
RES 408
RES 411 412 415 416 419 426 428 429
RES 432
RES 482 555 588 610
RES 612
RES 620 628
RES 645
RES 664 666
RES 685
RES 692
RES 694 695
RES 700
RES 740 745
RES 747
RES 829 830 835 861
RES 864 864 867 867 871 875 878 879 881 881 884 889
RES 892 893 895 895 897 898 900 900 904 906 909 909
RES 913
END
END
2967 3295 0000 0000 0 0 2 1.00000 0.00000
0610.00000 999.99900 610.00000 2.00000 0 0
2967 13906 0000 0000 0 0 1 1.00000 1.00000
0610.00000 999.99999 610.00000 999.99999 0 0
Received on Mon Oct 21 2002 - 19:18:10 PDT
