Re: Cannot find bond parameters

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 28 2011 - 11:09:12 CDT

On Tue, Jun 28, 2011 at 12:03 PM, Gayatri Rathod <rathod12g_at_gmail.com> wrote:
> Using VMD, I merged a bombolitin4 molecule that I built using Molefacture
> with 10 RDX molecules (built on Avogadro) using Merge Structures under
> Extensions -> Modeling.

but where did you get the atom types and force field
parameters for your molecule?

> This ended with the completed system pdb and psf files. I used the required
> conf file to equilibrate the system (after solvating and ionizing), but the
> following error showed up:
>
> UNABLE TO FIND BOND PARAMETERS FOR C H <ATOMS 1 6>

this is likely a consequence of not having proper atom types assigned.
you cannot just take some coordinate file and convert it into a pdb/psf
combo without defining all the proper atom types, assigning (partial)
charges, adding topology information and so on. this is what is usually
done by tools like psfgen using a residue/molecule topology template
database.

cheers,
     axel.
> I checked the structures for the molecules in the system, I'm sure they are
> correct before solvation - I don't know if they are correct after
> simulation.
>
> Where is the error and how do I fix it?
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:30 CST