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

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Fri Feb 27 19:10:01 CET 2004


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 !  ^&^
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################
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
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk




More information about the gromacs.org_gmx-users mailing list