VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 03 2011 - 17:51:20 CST

Please do note that NNEU/CNEU are not physically accurate in neutral
aqueous solution, and would almost never occur together in a real
protein... if you're trying to simulate only a fragment of a larger
protein and want chemically reasonable neutral termini, ACE/CT3 are
probably better choices. NNEU/CNEU are in there primarily for
simulations at extreme pH.
Best,
Peter

On 03/03/2011 04:13 PM, Tim Travers wrote:
>
> 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
> <mailto: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>
> [mailto: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 <mailto: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///
>
>
>
>
>
>