[gmx-users] grompp error: Unknown bond_atomtype

Justin Lemkul 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.
Assistant Professor
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


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