Homa Azizian wrote:
Hi Justin and all
when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce
with OPLS force field.
it seems that the protein has the charge of -3, while the ligand has the
charge of 0.890 and finally it prints that the final charge is -2.11. I
neutralized this charge with 2 NA+ so -0.11 charge remain (sorry for my
mistake this is 0.11 not 0.08).
So you should go and look at this ligand's topology and see where the
charge is going wrong. The partial charges should at least vaguely
correlate with chemical intuition.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
