[gmx-users] a question for generating a *.top file using pdb2gmx
spoel at xray.bmc.uu.se
Fri Feb 27 20:58:00 CET 2004
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!
> Have a good day ! ^&^
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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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