Bill Miller III wrote:
> Are there any error or warning messages in any of the output files,
> specifically either the standard error file, or in any of the _MMPBSA_*mdout
> files?
>
> -Bill
>
> On Mon, Jun 13, 2011 at 6:25 AM, <zw258.cam.ac.uk> wrote:
>
>
>> Jason Swails wrote:
>>
>>> Ah, it appears as though nab cannot handle a chamber-created topology
>>>
>> file,
>>
>>> which makes sense. The CHARMM-specific potential terms are not coded
>>>
>> into
>>
>>> nab.
>>>
>>> To fix this, you *must* have Amber11, and put the variable "use_sander=1"
>>> in
>>> your MMPBSA.py input file.
>>>
>>> Does this work?
>>>
>>> All the best,
>>> Jason
>>>
>>>
>>>
>> Hi Jason,
>> "use_sander=1" seems worked until I got this "Segmentation fault". Any
>> suggestions?
>> ******************************
>> Beginning GB calculations with sander...
>> calculating complex contribution...
>> calculating receptor contribution...
>> Segmentation fault
>> Error: sander error during GB calculations!
>> NOTE: All files have been retained for debugging purposes. Type
>> MMPBSA.py --clean to erase these files.
>> make: *** [cal] Error 1Beginning GB calculations with sander...
>> **********************************
>>
>> Best,
>> Zhi
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
>
I did not find any error information, but the _MMPBSA_receptor_gb.mdout
file looks strange. Please find the enclosed mdout file.
Regards,
Zhi
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 06/12/2011 at 23:16:19
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_gb.mdin
| MDOUT: _MMPBSA_receptor_gb.mdout
|INPCRD: _MMPBSA_dummyreceptor.inpcrd.1
| PARM: /home/zw258/apelin_npt/mmpbsa/input/rec.prmtop
|RESTRT: _MMPBSA_.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_receptor.mdcrd
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, ntb=0, surften=0.0072,
extdiel=78.3, ncyc=0, cut=999.0,
gbsa=1, saltcon=0.1, imin=5, igb=2,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/03 Time = 12:02:08
NATOM = 4845 NTYPES = 36 NBONH = 2431 MBONA = 2483
NTHETH = 5459 MTHETA = 3387 NPHIH = 9106 MPHIA = 4422
NHPARM = 0 NPARM = 0 NNB = 26758 NRES = 301
NBONA = 2483 NTHETA = 3387 NPHIA = 4422 NUMBND = 70
NUMANG = 154 NPTRA = 282 NATYP = 36 NPHB = 0
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Force field information read from topology file:
| CHARMM 31 *> CHARMM22 All-Hydrogen Topology File for Proteins and Lipi
|
|CHARMM: CHARMM force field in use.
|CHARMM: Overriding default value of chngmask.
|CHARMM: Setting chngmask = 0.
| Memory Use Allocated
| Real 350510
| Hollerith 14838
| Integer 445262
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 4535 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
|CHARMM: Reticulating splines.
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
* CHARMM I/O FILE
General flags:
imin = 5, 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 = 2, nsnb = 99999
ipol = 0, gbsa = 1, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00720
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.30000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1, ncyc = 0, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.4275E+03 1.7243E+01 1.2740E+02 C 2796
BOND = 1040.0884 ANGLE = 2381.7844 DIHED = 1645.7510
UB = 289.3229 IMP = 139.9575 CMAP = -321.3139
VDWAALS = -2003.7683 EEL = -15215.3267 EGB = -4208.2116
1-4 VDW = 1087.3598 1-4 EEL = 11586.4128 RESTRAINT = 0.0000
ESURF = 150.3995
minimization completed, ENE= -.34275440E+04 RMS= 0.172428E+02
minimizing coord set # 2
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.4969E+08 5.8699E+05 1.1195E+07 CB 4218
BOND = 84108538.3198 ANGLE = 353387.5250 DIHED = 11434.9221
UB = 8589527.3130 IMP = 55504.3420 CMAP = -216.6790
VDWAALS = 46280787.4421 EEL = -3158.3095 EGB = -7406.0076
1-4 VDW = 10313048.8075 1-4 EEL = -7392.8810 RESTRAINT = 0.0000
ESURF = 179.3359
minimization completed, ENE= 0.14969423E+09 RMS= 0.586993E+06
minimizing coord set # 3
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 6.4764E+11 1.2582E+11 7.7483E+12 SD 2775
BOND = ************* ANGLE = 366297.3107 DIHED = 11296.9506
UB = 9182436.7959 IMP = 58870.6580 CMAP = -384.8396
VDWAALS = ************* EEL = -2461.3617 EGB = -8591.1324
1-4 VDW = 10180832.1942 1-4 EEL = -8528.3679 RESTRAINT = 0.0000
ESURF = 257.2718
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Received on Mon Jun 13 2011 - 05:30:03 PDT
