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

[Zhen Qin]

Thank you. I tried. but the PRODRG deleted many H atoms from my input with a
lot of warning. And my protein is too big for it. There are more than 500
hundred atoms in the protein. Any other suggestions?

-Zhen
On Fri, 27 Feb 2004, Daan van Aalten wrote:

>
> Hi Zhen
>
> You could try putting the whole thing into the PRODRG server if you're OK
> with using the ffgmx ff.
>
> Daan
>
> On Fri, 27 Feb 2004, 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?
> >
> >  Thank you very much!
> >
> > -Zhen
> >
> > Have a good day !  ^&^
> >
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>
> ##############################################################################
> Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
> School of Life Sciences                E-mail: see WWW page
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