Re: Problem regarding the psfgen

From: Vibhor Agrawal (vibhora_at_g.clemson.edu)
Date: Fri Jun 07 2013 - 15:33:38 CDT

Hello Jack

Sorry i didn't pasted the code .
This is the one I used.

package require psfgen
topology ../top all27 prot lipid.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias atom HOH O OH2
pdbalias residue HOH TIP3

foreach S { PA } {
segment S {pdb $S.pdb
first ACE
last CT3
}}

On Fri, Jun 7, 2013 at 4:02 PM, Jack Bulat <jack.bulat_at_gmail.com> wrote:

> 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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