[gmx-users] mkyaw exectable file for TIP4P

David spoel at xray.bmc.uu.se
Sun Nov 23 11:00:01 CET 2003

On Sat, 2003-11-22 at 22:08, Yuhua Song wrote:
> Hi, David:
> I see the mailing list on July 1, 2003, you mention to use mkyaw program to
> add dummy atom to the crystall water generated from Pdb2gmx.
> Unfortunately, my computer did not have the exectable mkyaw program and the
> superuser is outof office. Could you kindly send me the exectable file for
> mkyaw for my use to add dummy atom to the crystall water?
> My computer system is Linux, I use Gromacs3.1.4.

you can compile it yourself in the gmx/src/contrib directory.
just go to the directory and write
make mkyaw
if you don't have write permissions there, you can copy the entire
directory to your home dir:
cd gmx/src
cp -r contrib ~
cd contrib
make mkyaw

Alternatively you can use the attached perl script.
> Thank you very much for your help.
> Yuhua
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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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