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Let's think we want to do a Gaussian optimisation. We first download the pdb coordinates of the query protein from the protein data bank. Then using Chimera software we add hydrogen and charge for the protein and save the file in .pdb format. And, we open this .pdb file using GaussView software define the basis set for the optimisation and save t as a gaussian input file (.gjf). This input file contains coordinates and the connectivity of the atoms of the protein. My question is in this method is it NECESSARY to add charge to the protein and isn't it necessary to have the connectivity of atoms in the .gjf file? When I started a gaussian job it terminated with an error QPErr --- A syntax error was detected in the input line. 1 3 1.0 2 1.0 4 1.0 5 1.0 Then I deleted all the lines that give connectivity and restarted the gaussian job. The job completed without an error. I thought that it is necessary to give the connectivity of the atoms in .gjf file. Am I wrong because my gaussian job completed even though I removed connectivity.

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    $\begingroup$ Does this answer your question? How can we restart an interrupted Gaussian job? $\endgroup$ Dec 1, 2022 at 8:34
  • $\begingroup$ @AndreaPellegrini Nope.. Still I could not find a solution to restart gaussan job from the interrupted point. And, the question asked here is to clear my doubts. $\endgroup$
    – PriZarah
    Dec 3, 2022 at 16:49

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Quick answer: No, connectivity is not required to start a Gaussian job.

The error message in your gjf file says

QPErr --- A syntax error was detected in the input line. 1 3 1.0 2 1.0 4 1.0 5 1.0

This simply means that your file was written in the wrong format. Take note of line spacing and such when manually preparing your gjf. If you can post your original gjf file, maybe we can help.

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