VMD-L Mailing List

From: Tim Travers (tstravers_at_gmail.com)
Date: Thu Mar 03 2011 - 15:13:33 CST

Good point, and I should have mentioned this. I'm using c35b2
(latest from http://mackerell.umaryland.edu/CHARMM_ff_params.html),
and this has NNEU and CNEU.

Tim

On Thu, Mar 3, 2011 at 3:32 PM, Mark Cunningham <cunningham_at_utpa.edu> wrote:

> Ms. Monroe:
>
>
>
> Going forward, you will need to provide more information than “I tried this
> and it didn’t
>
> work.” It would be helpful for you to post your input file and the output
> (or at least the
>
> relevant part of the output) for folks on the list to be of more help.
>
>
>
> Patching is a process by which psfgen, not vmd, modifies the atoms and
> bonds in
>
> a model structure. Your psfgen input should have blocks like
>
>
>
> segment PA { ! This defines a new PSF segment
>
> first NTER ! This says that the N-terminal
> amino acid ends in NH3+
>
> last CTER ! This says that the C-terminal
> amino acid ends in COO-
>
> pdb file_name1.pdb ! This is a file in PDB format that specifies the
> amino acid sequence
>
> }
>
> coordpdb file_name2.pdb PA ! This says read atomic coordinates from this
> file (not necessarily the same as the other)
>
>
>
> From your message, I’m assuming that psfgen failed but NTER and CTER are
> the correct CHARMM names
>
> for the patches. There are no CHARMM PRES types of NNEU or CNEU, at least
> not in my c32b1 directories.
>
> If they have been released recently, I will stand corrected. So, your
> second attempt failed because those
>
> names don’t exist in the CHARMM releases. It could be that NNEU and CNEU
> are defined locally, so you
>
> would have to include that topology file in addition to the standard CHARMM
> files. Without more information, I cannot offer better advice than to look
> at the psfgen output to see why it is unhappy.
>
>
>
> Good luck,
>
>
>
> Mark Cunningham, Associate Professor
>
> The University of Texas-Pan American
>
> 956-665-2171 (office) 956-665-2423 (fax)
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Ashlynne Monroe
> *Sent:* Thursday, March 03, 2011 10:41 AM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: capping or patching protein ends
>
>
>
> I have to cap/patch the ends of my protein. I tried to use the NTER and
> CTER sequence but it just killed my psf basically. So I looked in charmm and
> found the appropriate sequence which is NNEU and CNEU but VMD doesnt
> recognize this, so how do i fix this problem. Im new to this whole computer
> research thing so I hope someone could help me. Thank you
>
>
>
> *Ashlynne***
>
>
>
>
>