[gmx-users] crystallographic_water

Xavier Periole x.periole at chem.rug.nl
Tue May 4 13:55:02 CEST 2004

neda mirsamadi wrote:

>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.
Sounds normal to me. After genbox you have to correct the
topol.top, which correspond to the original one. You also can
ask genbox to generate to topol.top but never used it.

>then energy minimization followed by position
>restraint  MD and final MD run.
>Is that all which I should do?
>thanking in advance,



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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