Bob Duke and David,
Thanks for your reply. Actually I was running the job on the same molecule
previously on SUN system and now I wanted to shift it to this UNIX
machine. but the behaviour is totally different. My molecule consists of a
protein along with an organic molecule. I had prepared the frcmod and
prepin files for ths=is organic molecule. Now when I load the molecule
after loading the prepin and frcmod files, it complains about some bond
and angle parameters also says that it can not read the entered parameters
for the dihedral angles. So I added the missing angle and bond parameters
and also removed the entered dihedral parameters. now it was able to load
the molecule and save the parameter and coordinate files. I dont know why
there is this difference. The frcmod file used by me previopusly is same
for working on all other machines (SUN, SGI-orign, linux).
Now coming to the problem of floating exception. the input files used is
as follows:
--------------------------------------------
&cntrl
imin=1,
maxcyc=6000, ncyc=4000, drms=0.001,
ntb=0, ntr=1, ipol=0,
cut=999, igb=1
ntpr=500, lastist=3000000,
&end
Group input for restrained atoms 15
RES 1 112
END
Group input for restrained atoms
15
RES 116 125
END
END
------------------------------------------------
The output which I got in responce to it is as follows:
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
Wed Jan 5 21:49:11 2005
File Assignments:
MDIN: bsa-nocut-gbmin1.in
MDOUT: bsa-nocut-gbmin1.out
|INPCRD: mod2.inpcrd
| PARM: mod2.prmtop
|RESTRT: bsa-nocut-gbmin1.rst
| REFC: mod2.inpcrd
Here is the input file:
&cntrl
imin=1,
maxcyc=6000, ncyc=4000, drms=0.001,
ntb=0, ntr=1, ipol=0,
cut=999, igb=1
ntpr=500, lastist=3000000,
&end
Group input for restrained atoms 15
RES 1 112
END
Group input for restrained atoms
15
RES 116 125
END
END
---------------------------------------------------------------------------
1. RESOURCE USE:
---------------------------------------------------------------------------Flags:
|
Warning: lastist only works when MEM_ALLOC is set
| at compile time. Resetting the size of the
| stack to the value from sizes.h: 2000000
| New format PARM file being parsed.
| Version = 1.000 Date = 01/03/05 Time = 22:26:52
NATOM = 9293 NTYPES = 15 NBONH = 4596 MBONA = 4774
NTHETH = 10574 MTHETA = 6442 NPHIH = 19691 MPHIA = 12015
NHPARM = 0 NPARM = 0 NNB = 51428 NRES = 602
NBONA = 4774 NTHETA = 6442 NPHIA = 12015 NUMBND = 53
NUMANG = 111 NPTRA = 43 NATYP = 40 NPHB = 0
IFBOX = 0 NMXRS = 37 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated Used
| Real 2000000 381385
| Hollerith 400000 56362
| Integer 3200000 452707
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
---------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
---------------------------------------------------------------------------General
flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 1, nsnb =
25
ipol = 0, gbsa = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 6000, ncyc = 4000, ntmin = 1
dx0 = 0.01000, dxm = 0.50000, drms = 0.00100
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Group input for restrained atoms (1-112)
GROUP 1 HAS HARMONIC CONSTRAINTS 15.00000
GRP 1 RES 1 TO 112
Number of atoms in this group = 1729
----- READING GROUP 2; TITLE:
Group input for restrained atoms (116-125)
GROUP 2 HAS HARMONIC CONSTRAINTS 15.00000
GRP 2 RES 116 TO 125
Number of atoms in this group = 144
----- END OF GROUP READ -----
---------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
---------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
---------------------------------------------------------------------------
4. RESULTS
---------------------------------------------------------------------------
The machine I am using is a digital unix with single processor and alpha
CPU. the OS version is 4.0 D. the amber version I am using is Amber-7 and
the compiler used GCC (g77). I even checked the installation by running
the test case but it passed all the tests.
I hope I am able to give all the details and address the problem well.
Thanks once again for your help.
Waiting to hear from you.
With best regards,
Anshul
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Received on Fri Jan 07 2005 - 04:53:00 PST
