did the Amber test cases pass?
2010/4/25 geyan <geyan.big.ac.cn>
> 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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Received on Sun Apr 25 2010 - 04:00:03 PDT
