Re: [AMBER] Error reading Ruthenium complex residue

From: Sanaa ALAbbad <salabbad79.gmail.com>
Date: Thu, 12 Oct 2017 10:56:11 -0600

Szymon,

Thanks.
Yes I did, and included all coordination parameters, force field, and
charges in frcmod and mol2 files. But I am wondering since I found these
errors if there are other errors too?

Sanaa

On Thu, Oct 12, 2017 at 10:51 AM, Szymon ┼╗aczek <szymonzaczek.gmail.com>
wrote:

> Dear Sanaa,
>
> have you considered using MCPB.py? It is a very robust and versatile
> tool implemented in AmberTools for obtaining force field parameters
> for metal ions. More info may be found in tutorial:
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm or in a
> paper by Li and Merz (DOI: 10.1021/acs.jcim.5b00674).
>
> Kind regards,
> Szymon Zaczek
>
> 2017-10-12 17:27 GMT+02:00 Sanaa ALAbbad <salabbad79.gmail.com>:
> > Dear Ambers,
> >
> > I defined Ru in the atomic_ions.cmd then with tleap created the library.
> > The complex included 98 atoms.
> > Then I generated inpcrd and prmtop.
> > I manually corrected the following in the prmtop:
> >
> > 1- tleap wrote the Ru atomic_number =-1 ! so I corrected to 44
> > 2- tleap assigned only 2 atoms for the complex in the
> (ATOMS_PER_MOLECULE)
> > section.
> > 3- I corrected the SOLVENT_POINTERS section too.
> >
> > The simulation went fine but destroyed the complex!!
> >
> > I checked the validity of the topology file and the error is ParmWarning:
> > ATOMS_PER_MOLECULE section corrupt! Molecules are not contiguous!
> > Is this error what cause this problem in the minimization?
> > in other words
> > Is there other parameters that I am not aware of that have to be
> corrected
> > in the topology files?
> >
> > Thanks for any help,
> >
> > Sanaa Al Abbad
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>
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Received on Thu Oct 12 2017 - 10:00:02 PDT
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