I generated the predicted structure of a dimer of proteins using AlphaFold2, but it has overlapped amino acids like the picture.
(PDB file: https://drive.google.com/file/d/1frFw6gH1rqvtZfVmubVm-thQ2lvli1lZ/view?usp=sharing )
Because of this, SMOG ( https://smog-server.org/cgi-bin/GenTopGro.pl ) returns an error `FATAL ERROR: Contact between atoms 356 451 below threshold distance with value 0.192` when using this PDB as an input.
What I came up with was performing energy minimization on the entire protein by MD simulation software like Gromacs or resolving a part of the amino acid sequence using molecular viewers or modeling software like Pymol.
Which is a better way or is there another way to solve this issue?
Prepare your downloaded PDB using Maestro (Free academic version), where Protein Preparation Wizard Fix the problem of overlapping atoms in PDB.
Kiran Lokhande
Thank you for the helpful answer.
I will install Maestro and try it.
By the way, there's some similar software such as Pymol and UCSF chimera, but is there any special reason you recommend Maestro?
I checked your PDB file with both VMD and UCSF chimera. I could not find overlaps or missing .....
Then i checked it with gromacs 5.1.1 and generate a topology file for it ( OPLAS FF)...
Could you please discuss about your exact problem, becuase i think you can minimize your this PDB file with out any problem in Gromacs or VMD or ....
I also checked your PDB file in text format and i could not find any overlap residues,
Please read SMOG help or tutorial for specific instruction of pdb file, hope this help you ....
Please check the attached files
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