[gmx-users] a question for generating a *.top file using pdb2gmx

[David]

On Sat, 2004-02-28 at 00:19, Zhen Qin wrote:
> Thanks for your suggestion. Another problem of my protein is, in pdb file,
> the cyclopropane part and its two neighbour amino acids are not connected.
> So, if i take them as one residue, I need to adjust the sequence of the
> atoms in pdb file. For some reason, I need to keep the pdb file as it is
> now. :(  Any other suggestions? Thank you very much!
> 
SO you  are saying that the cyclopropane is somewhere else in the
sequence, say residue 102 and that you need to insert it between res. 53
and 54?

Is the structure at least correct?

If so, you can make a residue of cyclopropane (rtp entry) and then use
the specbond.dat file to indicate that bonds should be made between your
amino acids (and which atoms) and cyclopropane. You enter a bondlength
for these, so that it will pick the right AA to bind to.


> -Zhen
> 
> Have a good day !  ^&^
> 
> On Fri, 27 Feb 2004, David wrote:
> 
> > On Fri, 2004-02-27 at 18:59, Zhen Qin wrote:
> > > Dear gromacs users,
> > >   I have a question for using pdb2gmx to generate a *.top file for a
> > > special protein. The protein looks like this:
> > > NH-(CO-amino acid-NH)n-CO-cyclopropane-CO-(NH-amino acid-CO)m-NH
> > >   The middle part is not a regular amino acids. I add the information
> > > of -CO-cyclopropane-CO- to ffoplsaa.rtp as a residue, which has two C
> > > terminal, and no N terminal.
> > >   However, when I used  "pdb2gmx -f protein.pdb -p protein.top -inter"
> > > to generate the protein.top file, the bond connections between the
> > > middle part and its neighbour residues were not established, neither
> > > were the corresponding bond angles or dihedrals. Do you have any
> > > suggestions for making a topology file for such kind of protein?
> > >
> > If your residue does not have NH group you have a problem. The next
> > simplest solution is to make a new residue comprising the residue before
> > and the cyclopropane.
> >
> >
> > >  Thank you very much!
> > >
> > > -Zhen
> > >
> > > Have a good day !  ^&^
> > >
> > > _______________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
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> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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