Hi Ross,thank you your reply.
I exhibit my input and output at the end of this email. The creating prmtop file is just following the Amber Tutorial,first load the pdb structure in tleap and get the prmtop file with the saveambparm command,during the whole step,no special happen. When I use the prmtop file adding water to run sander in explicit solvent,the programm keeps working,while now in implicit water,crashing.
The input and output is as follows.It maybe a little long,appreciate your patience.
Minimization of the entire molecular system
&cntrl
imin=1,
maxcyc = 5000,
ncyc = 250,
cut = 12,
ntb=0,
igb=1
&end
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 04/22/2010 at 16:27:37
[-O]verwriting output
File Assignments:
| MDIN: min.in
| MDOUT: min1.out
|INPCRD: com.crd
| PARM: com.top
|RESTRT: min1.rst
| REFC: com.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
Minimization of the entire molecular system
&cntrl
imin=1,
maxcyc = 5000,
ncyc = 250,
cut = 12,
ntb=0,
igb=1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/09/10 Time = 22:26:16
NATOM = 4055 NTYPES = 17 NBONH = 1902 MBONA = 2225
NTHETH = 4311 MTHETA = 3102 NPHIH = 8513 MPHIA = 7264
NHPARM = 0 NPARM = 0 NNB = 22207 NRES = 247
NBONA = 2225 NTHETA = 3102 NPHIA = 7264 NUMBND = 54
NUMANG = 121 NPTRA = 63 NATYP = 30 NPHB = 0
IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 260173
| Hollerith 24579
| Integer 230868
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 3030 kbytes
| 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 = 50, 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, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 5000, ncyc = 250, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file 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
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 0.0000E+00 H5T 1
BOND = 156.7901 ANGLE = 1203.9996 DIHED = 2628.4433
VDWAALS = ************* EEL = -16114.0902 EGB = NaN
1-4 VDW = 871.3984 1-4 EEL = 4688.0962 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
271 NaN NaN 0.0000E+00 H5T 1
BOND = NaN ANGLE = NaN DIHED = 12512.1894
VDWAALS = 0.0000 EEL = 0.0000 EGB = -66813.9317
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.03 ( 0.08% of Total)
| Calc gb radii 7.20 (23.77% of Gen B)
| Calc gb diag 14.01 (46.22% of Gen B)
| Calc gb off-diag 9.10 (30.01% of Gen B)
| Gen Born time 30.31 (100.0% of Nonbo)
| Nonbond force 30.31 (96.13% of Force)
| Bond/Angle/Dihedral 1.19 ( 3.79% of Force)
| Other 0.03 ( 0.08% of Force)
| Force time 31.53 (100.0% of Runmd)
| Runmd Time 31.53 (95.13% of Total)
| Other 1.58 ( 4.78% of Total)
2010-04-25
geyan
发件人： Ross Walker
发送时间： 2010-04-24 13:56:43
收件人： 'AMBER Mailing List'
抄送：
主题： RE: [AMBER] about IGB
Hi Geyan,
We'd need to see your input and output files to be able to help more. You
may have a bad starting structure that is being made worse when using GB.
How did you create your prmtop file?
Have you tried running the test cases to make sure everything works?
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of geyan
> Sent: Friday, April 23, 2010 6:09 PM
> To: amber-all
> Subject: [AMBER] about IGB
>
> Has anybody met this problem before?when performing sander by turning
> on the IGB flag,in my case doing minimization with IGB=1,I got the err
> output maily printed NaN and the rst file produced all reads NaN.As
> long as I turn it off,everything becames OK.Does anybody know what is
> wrong and how to figure it out?
> Due to my negligence to clean up my Inbox of my email,I release
> this issue again,sorry.
> appreciate anyone's help.
> --------------
> geyan
> 2010-04-24
>
>
>
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> AMBER mailing list
> AMBER.ambermd.org
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Received on Sun Apr 25 2010 - 02:00:02 PDT
