<div>Satyan sharma and Mark</div>
<div>I see and get it.</div>
<div>thank you for your help<br><br> </div>
<div><span class="gmail_quote">On 4/27/08, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. question (Satyan Sharma)<br><br><br>----------------------------------------------------------------------<br>
<br>Message: 1<br>Date: Sun, 27 Apr 2008 11:53:23 +0300 (EEST)<br>From: Satyan Sharma <<a href="mailto:satyan@sun3.oulu.fi">satyan@sun3.oulu.fi</a>><br>Subject: [gmx-users] question<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:Pine.GSO.4.58.0804271145280.24144@sun3.oulu.fi">Pine.GSO.4.58.0804271145280.24144@sun3.oulu.fi</a>><br>Content-Type: TEXT/PLAIN; charset=US-ASCII<br><br>shahrbanoo karbalaee wrote:<br>><br>
> Dear<br>><br>> I donot get your answer.I have a peptide with NH2 bond in C terminal.Can<br>> I run MD with gromacs generally ?.or It shall know that as modified<br>> residue.<br>> when I run it I have this error: I donot find c for 14 residue.(it is<br>
> NH2 in c terminal).<br><br>Though it would not harm if you read chapter5 of manual before diving into<br>simulaitons. Mark is right, in the sense that people have to take time out<br>to answer you queries, when you dont have time to ask quetion with<br>
details.<br>To help you out, heres what I would do.<br>Lest say you have glycine in C terminus:<br>ATOM 10779 N GLY D3290 78.590 153.920 -4.727 1.00 39.48<br>ATOM 10780 CA GLY D3290 77.333 154.511 -4.322 1.00 39.26<br>
ATOM 10781 C GLY D3290 76.169 153.551 -4.502 1.00 39.05<br>ATOM 10782 O GLY D3290 75.018 153.908 -4.242 1.00 39.50<br>END<br><br>Add the N of NH2 and your modified file will be now:<br>ATOM 10779 N GLY D3290 78.590 153.920 -4.727 1.00 39.48<br>
ATOM 10780 CA GLY D3290 77.333 154.511 -4.322 1.00 39.26<br>ATOM 10781 C GLY D3290 76.169 153.551 -4.502 1.00 39.05<br>ATOM 10782 O GLY D3290 75.018 153.908 -4.242 1.00 39.50<br>ATOM 10783 N NH2 D3291 76.460 152.331 -4.946 1.00 38.03<br>
where Atom 10783 would be NH2 terminus. You can add this NH2 using any<br>graphics program .. or you can even modify one of the O in COO- terminus.<br><br>Now run pdb2gmx with -ter option and select option 2 for Cterminus like<br>
below<br><br>Opening library file<br>/share/apps/gromacs-3.3.1/share/gromacs/top/specbond.dat<br>5 out of 5 lines of specbond.dat converted succesfully<br>Select N-terminus type (start)<br>0: GLY-NH3+<br>1: NH2<br>2: None<br>
1<br>N-terminus: NH2<br>Select C-terminus type (end)<br>0: COO-<br>1: COOH<br>2: None<br>2<br>C-terminus: None<br>Now there are 2 residues with 9 atoms<br>Making bonds...<br><br>Thats all...Hope it helps<br><br>-Satyan<br>
<br><br>>"NH2 bond in C terminal" doesn't yet make any<br>sense.<br><br>>Mark<br><br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br>
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<br>End of gmx-users Digest, Vol 48, Issue 95<br>*****************************************<br></blockquote></div><br><br clear="all"><br>-- <br>sh-karbalaee