[gmx-users] Re: gmx-users Digest, Vol 48, Issue 95

[shahrbanoo karbalaee]

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:
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> Today's Topics:
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>   1. question  (Satyan Sharma)
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> ----------------------------------------------------------------------
>
> 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
>
>
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> End of gmx-users Digest, Vol 48, Issue 95
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-- 
sh-karbalaee
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