From: Jack Bulat (jack.bulat_at_gmail.com)
Date: Mon Jun 10 2013 - 12:21:32 CDT
Hey Vibhor,
Sorry for the delay. Here's what I've got:
> Info: generating structure...psfgen) Info: skipping improper N-C-CA-CD at beginning of segment.
In the topology file, there's an entry for an improper term under RESI PRO (the standard proline residue):
IMPR N -C CA CD
As far as I understand it, this entry is there by default, used whenever proline is in the middle of the chain and connected to a preceding (N-terminal) residue. Seeing as how you don't have any preceding residue (proline is N-terminal), this term is skipped by psfgen. In other words, this is fine.
> psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
Here's the corresponding entry in the topology file:
CMAP -C N CA C N CA C +N
Same with this. Note the presence of a minus sign in front of C. This seems to indicate the preceding carbonyl carbon (which is absent). Again, totally normal.
> psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
> psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
These are the terms corresponding to these comments:
IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
Again, preceding C is absent, so psfgen ignores this. Totally normal.
Now, I don't know what the last (C-terminal) residue looks like (cause you didn't tell me yet); however, I bet that the rest of the comments made by psfgen correspond to the analogous default terms that are skipped because of the C-terminal residue. For example, the comment,
> psfgen) Info: skipping bond C-N at end of segment.
probably corresponds to a lack of a carbonyl carbon-nitrogen amide bond (again, since the residue is a terminal residue).
At the end of the day, if you're able to coordinate the segment you're making with the structure, do guesscoord with no errors, and then do 'regenerate angles dihedrals' (something that, for certain patches, you ABSOLUTELY MUST DO to make it all work out in NAMD), you should be fine.
I'd encourage you to look through the topology file yourself and justify for yourself that these comments don't correspond to anything out of the ordinary. From my experience, as long as you don't have explicit "Warning:" messages or errors, you should be fine. But it's good to always double check, of course.
Hope this helps!
Jack
On Jun 8, 2013, at 12:17 PM, Vibhor Agrawal <vibhora_at_g.clemson.edu> wrote:
> 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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