Re: Problem regarding the psfgen

From: Vibhor Agrawal (vibhora_at_g.clemson.edu)
Date: Sat Jun 08 2013 - 14:17:52 CDT

Hey Jack !

Thanks for the help mate I used ACP instead of ACE and patched it .That was
one of the issue .What it is troubling me is the improper bonds at the
begining and at the end of the segment.

I don't know how to deal with them.Do let me know if you have any idea.

Thanks
Vibhor

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

On Fri, Jun 7, 2013 at 4:51 PM, Jack Bulat <jack.bulat_at_gmail.com> wrote:

> Hey Vibhor,
>
> Ok, I see. I believe that what's happening is that, since the first
> residue is a proline, the improper angle for patch ACE can't be set. Here's
> the line in the top file that specifies this:
>
> IMPR N CY CA HN
>
> That's why you get the error:
>
> > psfgen) Warning: add improper failed in patch ACE
>>
>
> And then it tells you that there's no such atom. This makes sense, since
> proline is a circularized amino-acid and so doesn't have the backbone
> hydrogen on the nitrogen. For clarification, "HN" suggests that it's the
> hydrogen that's of the type that's attached to nitrogens.
>
> I'd suggest using the patch ACP, which has been specifically designed for
> proline. It acetylates proline.
>
> Let me know if that works.
>
> Cheers!
> Jack
> UC Berkeley
>
> P.S.: Stupid proline!
>
>
> On Jun 7, 2013, at 1:33 PM, Vibhor Agrawal <vibhora_at_g.clemson.edu> wrote:
>
> 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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