Hello,
I have missing atoms and residues in my PDB file and I need to fix them in order to proceed with pdb2gmx (GROMACS). I used swissModel but the generating file is lacking the final residue in Cter, I verified the template, added "TER" between my 2 chains but it doesn't work! I had the idea to complete this residue manually since I have its atomic coordinates but I don't know if it's a good idea or not specially that the last column in the pdb file generated by Swiss Model contain other values than the temperture factor I think.
Any suggestions? I'll be very gratful.
Hi Zeineb,
How many residues having missing atoms?
The best way is to open the original file in Chimera, and replaced the residues with missing atoms to the best suitable rotamer of the same amino acid. There is a tutorial on Youtube regarding the introduction of mutations in PDB using Chimera. the same way you can mutate the missing coordinates with rotameric forms. It will solve the issue.
Yes, you can simple add the coordinates, and I hope pdb2gmx will ignore that column (though i am not sure). You can read the pdb2gmx -h.
HTH,
Hi Zeineb
You can use http://lorentz.dynstr.pasteur.fr/pdb_hydro.php server to fix side chains and residues
Hi, thank you very much for your answers, I finally used MODELLER and gave me good results.
All the best for you.
Zeineb.
Hi Zeineb
I find using chimera + modeller the best way since just using modeller program seems harder to me. for more information you can read chimera tutorial or search some movies about it in YouTube.
Hi Zeineb,
Can you please help me how you fixed the issue using modeller. I did follow the missing residue tutorial of modeller but did not get the actual results.
Thanks
The easiest way to fix the missing atoms is that you can open your PDB structure in swiss PDB viewer software and then save the structure without doing any extra action. Then you can use pdb2gmx.
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