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

[Zhen Qin]

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!

-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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