Re: Problem regarding the psfgen

From: Jack Bulat (jack.bulat_at_gmail.com)
Date: Fri Jun 07 2013 - 15:02:58 CDT

Hey Vibhor,

I've successfully used these patches before, and would like to help. But could you please paste in a chunk of the code you wrote that produced this output? Otherwise, it's difficult to narrow down what the problem could be.

Thanks,
Jack Bulat
UC Berkeley

On Jun 7, 2013, at 12:55 PM, Vibhor Agrawal <vibhora_at_g.clemson.edu> wrote:

> I was capping the end of the protein with the ACE and CT3 and was creating psfgen but there was error .Please help
>
> Thanks
> Vibhor
>
>
>
>
> psfgen) building segment S
> psfgen) reading residues from pdb file PA.pdb
> psfgen) extracted 300 residues from pdb file
> psfgen) setting patch for first residue to ACE
> psfgen) setting patch for last residue to CT3
> psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-CD at beginning of segment.
> psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
> psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
> psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
> psfgen) Info: skipping bond C-N at end of segment.
> psfgen) Info: skipping improper C-CA-N-O at end of segment.
> psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
> psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
> psfgen) Info: skipping conformation N-CA-C-O at end of segment.
> psfgen) Info: skipping conformation N-CA-C-N at end of segment.
> psfgen) no atom HN in residue PRO:1 of segment S
> psfgen) Warning: add improper failed in patch ACE
> psfgen) no atom HN in residue PRO:1 of segment S
> psfgen) Warning: add conformation failed in patch ACE

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