Satyan sharma and Mark I see and get it. thank you for your help
On 4/27/08, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Send gmx-users mailing list submissions to > [email protected] > > 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 > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > 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 <[EMAIL PROTECTED]> > Subject: [gmx-users] question > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > 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 > [email protected] > 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
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