VMD-L Mailing List

From: Tim Travers (tstravers_at_gmail.com)
Date: Thu Mar 03 2011 - 11:39:11 CST

Hello,

I'm not sure how you mean by VMD not recognizing this. I regularly use
neutral patches, via the psfgen
plugin of VMD. You can follow the tutorial at

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html

and at step 6, when you create a segment for your PDB via:

segment U {pdb ubq.pdb}

you can do this instead:

segment U {
pdb ubq.pdb
first NNEU
last CNEU
}

just replace 'U' with your desired segment name (I usually just use P), and
'ubq.pdb' with
the name of your PDB file.

Hope this helps,
Tim

On Thu, Mar 3, 2011 at 11:40 AM, Ashlynne Monroe <
babysbutton070212_at_yahoo.com> wrote:

> 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*
>
>
>