[gmx-users] grompp error: Unknown bond_atomtype
jalemkul at vt.edu
Tue Apr 9 17:32:52 CEST 2019
On 4/1/19 5:28 AM, vicolls at fizyka.umk.pl wrote:
> Dear Professor Lemkul,
> You have written that I mix amber and charmm forcefields. It is kinda
> intiguing, becuase I downloaded lipid parameteres in amber and the
> atom names in the files are exactly the same as charmm-gui pdb output.
Atom *names* in a coordinate file are an entirely different concept from
atom *types* in a force field parameter set.
> I attach membrane pdb and parameter file. I would be very thankfull if
> you would take a look and judge if these are consistent. As I said -
> pdb2gmx worked well with these files, only grompp got troubles with
> "Unknown bond_atomtype CTL3". If CTL3 atom is characteristic for
> charmm ff why these names are used in amber files?
I don't have nearly enough information to help you answer that question.
But you've got an unknown atom type in your topology, that much is clear.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users