Re: [AMBER] Can I include Mg ions in receptor mask when using

From: Pengfei Li <>
Date: Mon, 19 Mar 2018 17:29:59 -0500

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: <>. ParmEd can also help for the checking.

Kind regards,

> On Feb 27, 2018, at 4:19 PM, Jie Zhu <> wrote:
> Hi, All,
> I had some issues when I ran 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,
> 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/", line 99, in <module>
> app.file_setup()
> File
> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/",
> 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/",
> 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/",
> line 467, in __init__
> self.Query()
> File
> "/home/jz347/Amber17Pure/lib/python2.7/site-packages/MMPBSA_mods/",
> 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 and did not include Mg in the receptor mask.
> This time 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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Received on Mon Mar 19 2018 - 16:00:02 PDT
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