On 5/17/12 10:48 AM, Lara Bunte wrote:
Hi
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
gives me errors like
ERROR 1 [file topol.top, line 233]:
No default Improper Dih. types
and so on. This line 233 is the starting of my empty [ dihedrals ] block. I
erase it by hand out of my topology, so that only the correct [ dihedrals ] out
of the .rtp and ffbonded.itp file are in the topology. After this grompp works
without error and even without any warning.
So the question how to force pdb2gmx to use only my [ dihedrals ] block is
important for me, because I don't like to erase it always by hand out of the
topol.top file.
This goes back to something that has been stated several times now, and was
discussed the other day. If pdb2gmx finds 4 atoms connected via bonds, it
assigns a dihedral to it. That's just physically real. If your force field
then doesn't have parameters for that particular interaction, you get the error
shown above. That doesn't mean you should go deleting things until grompp
"works" because what will result will likely be senseless.
If your "empty" (which is not really empty, as we've been saying) dihedrals are
causing the problems, then you need to add parameters for them in ffbonded.itp
or in the topology itself, not hack the topology apart.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
