Dear Elvis
The output file from sander complex_gb.mdout does not show any error
message but only an info that "old style inpcrd file found". Could it be a
reason of error?
Output is as follows:-
Executable path: /home/rcms/Downloads/Amber/amber20/bin/sander
| Working directory: /media/rcms/38E25F25E25EE6A2/20nscomplete/MMPBSA
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_gb.mdin
| MDOUT: _MMPBSA_complex_gb.mdout.0
|INPCRD: _MMPBSA_dummycomplex.inpcrd
| PARM: complexdry.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
ntb=0, nsnb=99999, cut=999.0, imin=5,
ncyc=0, igb=2, saltcon=0.1,
surften=0.0072, extdiel=80.0,
dec_verbose=0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 01/19/21 Time = 16:31:56
NATOM = 8076 NTYPES = 18 NBONH = 3983 MBONA = 4187
NTHETH = 9054 MTHETA = 5686 NPHIH = 18423 MPHIA = 17621
NHPARM = 0 NPARM = 0 NNB = 44535 NRES = 502
NBONA = 4187 NTHETA = 5686 NPHIA = 17621 NUMBND = 90
NUMANG = 202 NPTRA = 208 NATYP = 54 NPHB = 0
IFBOX = 0 NMXRS = 73 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 1389724
| Hollerith 24732
| Integer 471193
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 12794 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 = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 2, nsnb =
99999
ipol = 0, gbsa = 0, 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
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
I am looking forward to your suggestions, please.
Regards
Sadaf
On Mon, 25 Jan 2021 at 09:47, Sadaf Rani <sadafrani6.gmail.com> wrote:
> Dear Elvis
> I added use_sander=1 in the input file as below:-
> Input file for running PB and GB
> &general
> endframe=2000, verbose=1,receptor_mask=":1-491",
> strip_mask=":Na+:WAT",use_sander=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
>
> However, I am getting an error with the complex prmtop file now as
> mentioned below:-
>
> Beginning GB calculations with
> /home/rcms/Downloads/Amber/amber20/bin/sander
> calculating complex contribution...
> File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
> <module>
> app.run_mmpbsa()
> File
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 156, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /home/rcms/Downloads/Amber/amber20/bin/sander failed with
> prmtop complexdry.prmtop!
> Exiting. All files have been retained.
>
> What else should I try to fix this error? Please guide me.
> Thanks in advance.
> Sadaf
>
> On Thu, 21 Jan 2021 at 12:53, Elvis A F Martis <martiseaf.elvismartis.in>
> wrote:
>
>> Hi
>> Try using use_sander = 1 in your control file.
>>
>> On Thu, 21 Jan 2021 at 12:50, Sadaf Rani <sadafrani6.gmail.com> wrote:
>>
>> > Dear Amber user
>> >
>> > I am doing MMPBSA calculations on a 20ns trajectory for protein and
>> ligand
>> > complex. I am getting error of cpptraj failed with ligand prmtop as
>> > mentioned below:-
>> > MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
>> complex.prmtop
>> > -cp complexdry.prmtop -rp protein_cofactordry.prmtop -lp G6P_n.prmtop -y
>> > Prod.crd
>> > Loading and checking parameter files for compatibility...
>> >
>> >
>> /home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py:603:
>> > UserWarning: receptor_mask overwritten with default
>> >
>> > warnings.warn('receptor_mask overwritten with default\n')
>> > cpptraj found! Using /home/rcms/Downloads/Amber/amber20/bin/cpptraj
>> > mmpbsa_py_energy found! Using
>> > /home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
>> > Preparing trajectories for simulation...
>> > 2000 frames were processed by cpptraj for use in calculation.
>> >
>> > Running calculations on normal system...
>> >
>> > Beginning GB calculations with
>> > /home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
>> > calculating complex contribution...
>> > calculating receptor contribution...
>> > calculating ligand contribution...
>> > File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
>> > <module>
>> > app.run_mmpbsa()
>> > File
>> >
>> >
>> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
>> > line 218, in run_mmpbsa
>> > self.calc_list.run(rank, self.stdout)
>> > File
>> >
>> >
>> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
>> > line 82, in run
>> > calc.run(rank, stdout=stdout, stderr=stderr)
>> > File
>> >
>> >
>> "/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
>> > line 475, in run
>> > raise CalcError('%s failed with prmtop %s!' % (self.program,
>> > CalcError: /home/rcms/Downloads/Amber/amber20/bin/cpptraj failed with
>> > prmtop G6P_n.prmtop!
>> >
>> > I am new in doing this calculation, could anyone please help me to
>> figure
>> > out the problem why I am getting this error and how should I fix it. Any
>> > suggestion would really be appreciated.
>> > Thanks in advance.
>> > Regards
>> > Sadaf
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> Best Regards
>> Elvis
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Sun Jan 24 2021 - 21:30:02 PST
