Tamas Horvath wrote:
As I understand, if there are "special" molecules in a pdb file, pdb2gmx
cannot convert it. However, PRODRG can create an *.itp file for that
molecule, so that I can include it in the generated topology file. But
how can I place the molecule in it's original position? Or even better,
how can I convert the original ("full") .pdb file for gromacs?
Where's the problem? pdb2gmx makes a .top file for your non-special
system, you #include the .itp file for your special part. There's
nothing about atomic positions yet.... have a look at a .top file. Now
grompp takes the .top and some file with atomic positions and makes a
.tpr file. Same general procedure as normal.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
