unnatural amino acid MMPBSA

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Sijie C

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Mar 28, 2021, 3:30:46 PM3/28/21
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Hi , i have run unnatural amino acid simulation and want to calculate the binding affinity for the new peptide-protein complex.  The program wont let me to process it because it cannot recognize the new type of amino acid. I am not familiar with AMBER so I don't know how to incorporate new type of AA into Leap program. Thanks for your help! Really appreciated 

Mario Sergio Valdes

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Mar 28, 2021, 3:40:28 PM3/28/21
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Hi and Welcome!

Could you give us a little more information?
How did you parameterize the amino acid? What force field did you use?
Did you try to use topology instead of structure? Try this method, you simply have to define the GROMACS topology with the -cp option, in addition to the command line you are using.

Best!
Mario S.

Sijie C

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Mar 28, 2021, 4:26:32 PM3/28/21
to Mario Sergio Valdes, gmx_MMPBSA
Hi Mario,

Thanks for your reply.  I parameterize the amino acid using SwissParm.  I am using charmm27. I used topology and structure. After you informed me the -cp option, I try to re-run but another issue was raised up due to topology.  I also attached my topology file for your reference. Thanks for your help!

The below is error message.

Best,
Sijie

/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/topologyobjects.py:2680: ParameterWarning: Overriding DihedralType in DihedralTypeList with same periodicity
  warnings.warn('Overriding DihedralType in DihedralTypeList '
/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/topologyobjects.py:2680: ParameterWarning: Overriding DihedralType in DihedralTypeList with same periodicity
  warnings.warn('Overriding DihedralType in DihedralTypeList '
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/bin/gmx_MMPBSA", line 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==1.4.0', 'console_scripts', 'gmx_MMPBSA')())
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-1.4.0-py3.9.egg/GMXMMPBSA/app.py", line 97, in gmxmmpbsa
    app.make_prmtops()
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-1.4.0-py3.9.egg/GMXMMPBSA/main.py", line 577, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-1.4.0-py3.9.egg/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/gmx_MMPBSA-1.4.0-py3.9.egg/GMXMMPBSA/make_top.py", line 295, in gmxtop2prmtop
    com_top = parmed.gromacs.GromacsTopologyFile(self.complex_temp_top, xyz=self.complex_str_file)
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 259, in __init__
    self.coordinates = f.coordinates
  File "/home/PHARMACY/chen.3428/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/structure.py", line 1699, in coordinates
    coords = coords.reshape((-1, len(self.atoms), 3))
ValueError: cannot reshape array of size 7614 into shape (4170,3)
Exiting. All files have been retained.

发件人: gmx_m...@googlegroups.com <gmx_m...@googlegroups.com> 代表 Mario Sergio Valdes <mariosergi...@gmail.com>
发送时间: Sunday, March 28, 2021 3:40:27 PM
收件人: gmx_MMPBSA <gmx_m...@googlegroups.com>
主题: Re: unnatural amino acid MMPBSA
 
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topol.top
topol_Protein_chain_A.itp
topol_Protein_chain_B.itp

Mario Sergio Valdes

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Mar 28, 2021, 4:53:15 PM3/28/21
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This error is related to the structure and groups that you defined. gmx_MMPBSA removes the waters and ions from the topology so if you define a group that has waters or ions (NA and CL) the number of atoms in the topology and in the structure will differ.
Regarding the amino acid, I'm not sure if it will work even if you can get the topology correctly since the types of atoms in this residue are probably not recognized in PB which is recommended in your case.

In any case, carefully review the groups you defined and the generated PDB files (_GMXMMPBSA_COM.pdb, etc) to verify that there is indeed a relationship between the two. If it still doesn't work, feel free to tell me and send me the files you use: tpr, ndx, xtc (only 10 frames), top, itp, and the receptor and ligand groups respectively so that I can review them.
Best!
Mario S.

Chen Sijie

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Mar 28, 2021, 10:12:16 PM3/28/21
to Mario Sergio Valdes, gmx_MMPBSA
Hi Mario,

After being fixed the number of coordinates, the system ran smoothly. Thanks very much for your help.

Best
Sijie

发送时间: Sunday, March 28, 2021 4:53:15 PM

Mario Sergio Valdes

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Mar 28, 2021, 11:38:12 PM3/28/21
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With pleasure. We are glad that our tool is useful to you.
Best!
Mario S.

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