[gmx-users] Re: gmx-users Digest, Vol 48, Issue 95
shahrbanoo karbalaee
shahrbanoo at gmail.com
Sun Apr 27 15:12:32 CEST 2008
Satyan sharma and Mark
I see and get it.
thank you for your help
On 4/27/08, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. question (Satyan Sharma)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 27 Apr 2008 11:53:23 +0300 (EEST)
> From: Satyan Sharma <satyan at sun3.oulu.fi>
> Subject: [gmx-users] question
> To: gmx-users at gromacs.org
> Message-ID: <Pine.GSO.4.58.0804271145280.24144 at sun3.oulu.fi>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> shahrbanoo karbalaee wrote:
> >
> > Dear
> >
> > I donot get your answer.I have a peptide with NH2 bond in C terminal.Can
> > I run MD with gromacs generally ?.or It shall know that as modified
> > residue.
> > when I run it I have this error: I donot find c for 14 residue.(it is
> > NH2 in c terminal).
>
> Though it would not harm if you read chapter5 of manual before diving into
> simulaitons. Mark is right, in the sense that people have to take time out
> to answer you queries, when you dont have time to ask quetion with
> details.
> To help you out, heres what I would do.
> Lest say you have glycine in C terminus:
> ATOM 10779 N GLY D3290 78.590 153.920 -4.727 1.00 39.48
> ATOM 10780 CA GLY D3290 77.333 154.511 -4.322 1.00 39.26
> ATOM 10781 C GLY D3290 76.169 153.551 -4.502 1.00 39.05
> ATOM 10782 O GLY D3290 75.018 153.908 -4.242 1.00 39.50
> END
>
> Add the N of NH2 and your modified file will be now:
> ATOM 10779 N GLY D3290 78.590 153.920 -4.727 1.00 39.48
> ATOM 10780 CA GLY D3290 77.333 154.511 -4.322 1.00 39.26
> ATOM 10781 C GLY D3290 76.169 153.551 -4.502 1.00 39.05
> ATOM 10782 O GLY D3290 75.018 153.908 -4.242 1.00 39.50
> ATOM 10783 N NH2 D3291 76.460 152.331 -4.946 1.00 38.03
> where Atom 10783 would be NH2 terminus. You can add this NH2 using any
> graphics program .. or you can even modify one of the O in COO- terminus.
>
> Now run pdb2gmx with -ter option and select option 2 for Cterminus like
> below
>
> Opening library file
> /share/apps/gromacs-3.3.1/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> Select N-terminus type (start)
> 0: GLY-NH3+
> 1: NH2
> 2: None
> 1
> N-terminus: NH2
> Select C-terminus type (end)
> 0: COO-
> 1: COOH
> 2: None
> 2
> C-terminus: None
> Now there are 2 residues with 9 atoms
> Making bonds...
>
> Thats all...Hope it helps
>
> -Satyan
>
>
> >"NH2 bond in C terminal" doesn't yet make any
> sense.
>
> >Mark
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 48, Issue 95
> *****************************************
>
--
sh-karbalaee
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080427/72113e7c/attachment.html>
More information about the gromacs.org_gmx-users
mailing list