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

[Daan van Aalten]

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
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