[gmx-users] crystallographic_water

neda mirsamadi nedamirsamadi at yahoo.com
Mon May 3 22:30:02 CEST 2004

Dear all
I would like to simulate a system including a protein
and crystallographic waters. I would like to specify
this crystallographic waters with another name like
WAT through out my simulation. First I tried to change
them in initial PDB file but after running pdb2gmx
they were renamed as SOL, so it failed. Then  I tried
the second procedures.
I copied spc.itp in my directory and rename it as
I run pdb2gmx and then rename all SOL to WAT in my
*.gro file. I added the line #include "WAT.itp" to my
*.top file and in the last line I changed SOL to WAT.
I run editconf.
But after running genbox in newly made *.top file I
had extra number of SOL molecules so I got an error
after running grompp that number of coordinates in
genbox.gro does not match with top files. So I
corrected the number of SOL in *.top.
then energy minimization followed by position
restraint  MD and final MD run.
Is that all which I should do?
thanking in advance,

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