Dear Amber User
I am trying to calculate binding energy between proteins and ligand for
that I used MMPBSA module of Amber Tools 16.
I generated topology for complex , receptor and ligand from my leap
generated topology file by the help of ante-MMPBSA.py.
ante-MMPBSA.py -p juma_hel_atp_wat.top -c juma-hel-comp.parm7 -r
juma-hel-rec.parm7 -l juma-hel-lig.parm7 -s :Na,WAT -n :atp
After running MMPBSA I got following error .
[rahman.centos7 juma-ATP]$ MMPBSA.py -O -i mmpbsa.in -cp
juma-hel-comp.parm7 -lp juma-hel-lig.parm7 -y juma_helatp_.nc -deo
decom-juma_helatp.dat -o mmpbsa_juma_helatp.dat
Loading and checking parameter files for compatibility...
File "/home/rahman/sware/ambtool16/amber16/bin/MMPBSA.py", line 98, in
<module>
app.loadcheck_prmtops()
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/MMPBSA_mods/main.py",
line 572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/readparm.py",
line 70, in LoadParm
parm = parm.view_as(AmberParm)
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/_amberparm.py",
line 477, in load_structure
self._check_section_lengths()
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/_amberparm.py",
line 1246, in _check_section_lengths
check_length('ATOMIC_NUMBER', natom, False)
File
"/home/rahman/sware/ambtool16/amber16/lib/python3.5/site-packages/parmed/amber/_amberparm.py",
line 1235, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG ATOMIC_NUMBER has 48937 elements; expected 7117
Exiting. All files have been retained.
[rahman.centos7 juma-ATP]$
I search in amber archives for this error and I found similar error (
http://archive.ambermd.org/201509/0099.html).
But it is mention in the mailing list it will fixed in the AmberTools 15.
Now I am using Amber Tools 16, still this bug is there or I am following
some wrong step in generating topology .
Thanks
Regards
Rahman
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Received on Fri Jun 10 2016 - 15:00:03 PDT
