[gmx-users] grompp error: Unknown bond_atomtype

[Justin Lemkul]

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

-- 
==================================================

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
http://www.thelemkullab.com

==================================================