[gmx-users] how to generate a .itp file wiht new bond?

David spoel at xray.bmc.uu.se
Wed Sep 24 21:57:01 CEST 2003

On Wed, 2003-09-24 at 21:00, jiancong wrote:
> Hello,
> In my structure, there is a new bond between NE2 of histidine and CE2 of
> tyrosine which are 3 amino-acid far from each other. How can I generate a
> itp file with this new bonding included?
You have to make a new entry in the specbond.dat file. Copy it to your
working directory and add a line:

HIS     NE2     1       TYR   CE2      1       0.14     HIS    TYR

Now pdb2gmx will look for bonds with a length of 0.14 nm between any
pair of HIS-NE2/TYR-CE2

You may have to make additional modifications to e.g. rtp and hdb files.

> Thanks,
> Jiancong
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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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