VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Thu Mar 03 2011 - 14:32:08 CST

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[http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys2/07.gif]