Relevant ParmEd commands can be found in the Pages 269-270 of the AMBER 2017 manual: http://ambermd.org/doc12/Amber17.pdf <http://ambermd.org/doc12/Amber17.pdf> (From term 14.2.2.40 to 14.2.2.48).
> On Mar 19, 2018, at 5:29 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Jie,
>
> It may be related to the way you set up the system. Maybe you can check whether everything is OK for the Mg2+ ion in your prmtop file. The prmtop file format can be found here: http://ambermd.org/formats.html <http://ambermd.org/formats.html>. ParmEd can also help for the checking.
>
> Kind regards,
> Pengfei
>
>> On Feb 27, 2018, at 4:19 PM, Jie Zhu <zhujiejz39.gmail.com <mailto:zhujiejz39.gmail.com>> wrote:
>>
>> Hi, All,
>>
>> I had some issues when I ran MMPBSA.py to calculate the free binding energy
>> of two proteins.
>>
>> One of the protein (receptor) has a Mg2+ ion coordinated with residues (D
>> and S) inside the protein. The ligand protein comes and binds to the
>> receptor by coordinating with the Mg2+ ion by a E residue. Therefore, in
>> the complex, the two proteins are connected by one Mg2+ ion so that Mg2+
>> ion is crucial for this binding.
>>
>> However, when I included Mg2+ in the receptor mask when running MMPBSA.py,
>> I got issues. The error information I got is as below:
>>
>>
>> Loading and checking parameter files for compatibility...
>> sander found! Using /home/jz347/Amber17Pure/bin/sander
>> cpptraj found! Using /home/jz347/Amber17Pure/bin/cpptraj
>> mmpbsa_py_nabnmode found! Using
>> /home/jz347/Amber17Pure/bin/mmpbsa_py_nabnmode
>> Preparing trajectories for simulation...
>> Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 7
>> Error: Box line=[ 69.184 25.640 44.865 69.883 24.944 46.082 70.198
>> ]
>> Error: Could not set up '_MMPBSA_complex.mdcrd.0' for reading.
>> Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
>> Error: Error(s) occurred during execution.
>> File "/home/jz347/Amber17Pure/bin/MMPBSA.py", line 99, in <module>
>> app.file_setup()
>> File
>> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/main.py",
>> line 156, in file_setup
>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
>> File
>> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
>> line 216, in make_trajectories
>> (trj_suffix, i) for i in range(size)], cpptraj)
>> File
>> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
>> line 467, in __init__
>> self.Query()
>> File
>> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
>> line 602, in Query
>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
>> TrajError: /home/jz347/Amber17Pure/bin/cpptraj failed when querying
>> _MMPBSA_complex.mdcrd.0
>> Exiting. All files have been retained.
>>
>> I'm sure that the ligand and receptor mask indexes are correct. I loaded
>> the _MMPBSA_complex.mdcrd.0 file in VMD and found that all structures were
>> messed up. Then I counted the atom in one snapshot of mdcrd file and found
>> that there is one residue less than my specified mask. I think the missing
>> atom must be the Mg ion.
>>
>> Then I ran another MMPBSA.py and did not include Mg in the receptor mask.
>> This time MMPBSA.py ran successfully. It seems that the Mg atom was causing
>> the box coords error, although I don't know why. However, in this
>> situation, the binding free energy calculated was positive. I think it
>> should be due to the repulsion of two proteins when the crucial Mg ion is
>> missing.
>>
>> My question is: Is there a way that I can include the Mg ion in the
>> receptor mask so that I can calculate the real binding free energy?
>>
>>
>> Best,
>> Jie
>> _______________________________________________
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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 19 2018 - 16:30:03 PDT
