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.
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