Along with the trailing mail Please find below the
_MMPBSA_complex_gb.mdout.0 files details:
#####################
File Assignments:
| MDIN: _MMPBSA_gb_decomp_com.mdin
| MDOUT: _MMPBSA_complex_gb.mdout.0
|INPCRD: _MMPBSA_dummycomplex.inpcrd
| PARM: com_nowat.prmtop
|RESTRT: _MMPBSA_restrt.0
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd.0
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, dec_verbose=1, ntb=0,
surften=0.0072, extdiel=80.0, ncyc=0,
cut=999.0, gbsa=2, saltcon=0.1,
imin=5, idecomp=1, igb=2,
/
Residues considered as REC
RRES 1 101
END
Residues considered as LIG
LRES 102 102
END
Residues to print
RES 1 102
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 09/07/20 Time = 23:58:25
NATOM = 1601 NTYPES = 24 NBONH = 802 MBONA = 808
NTHETH = 1822 MTHETA = 1091 NPHIH = 3630 MPHIA = 3421
NHPARM = 0 NPARM = 0 NNB = 8813 NRES = 102
NBONA = 808 NTHETA = 1091 NPHIA = 3421 NUMBND = 58
NUMANG = 125 NPTRA = 144 NATYP = 34 NPHB = 0
IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
| Memory Use Allocated
| Real 147887
| Hollerith 4907
| Integer 239059
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 2108 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
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 5, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 1, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 2, nsnb =
99999
ipol = 0, gbsa = 2, 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 = 80.00000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1, ncyc = 0, ntmin = 1
dx0 = 0.01000, drms = 0.00010
#######################################
On Tue, Feb 9, 2021 at 10:55 AM Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Thank you for the reply.
>
> I tried running the decomposition with the serial version of MMPBSA.py but
> again I got the same error.
>
> #####################################33
> Loading and checking parameter files for compatibility...
> sander found! Using /apps/scratch/compile/amber18/bin/sander
> cpptraj found! Using /apps/scratch/compile/amber18/bin/cpptraj
> Preparing trajectories for simulation...
> 25001 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /apps/scratch/compile/amber18/bin/sander
> calculating complex contribution...
> bad atom type: i
> File "/apps/scratch/compile/amber18/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /apps/scratch/compile/amber18/bin/sander failed with prmtop
> com_nowat.prmtop!
> Exiting. All files have been retained.
> #############################################
>
> Can you please try to solve the error.
> Why with the same *.prmtop and *.mdcrd GBSA and PBSA is running and
> getting the results but showing error while running decomp?
>
> Thanks
>
> On Fri, Feb 5, 2021 at 7:18 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Feb 05, 2021, Nisha Amarnath Jonniya wrote:
>>
>> >CalcError: /apps/scratch/compile/amber18/bin/sander failed with prmtop
>> >com_nowat.prmtop!
>> >Error occured on rank 2.
>> >Exiting. All files have been retained.
>>
>> Please look at the mdout files for the sander run that used
>> com_nowat.prmtop. Also, try a test run with the serial version of
>> MMPBSA.py, to see if that helps, or maybe gives better error messages.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Feb 08 2021 - 22:00:02 PST
