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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 12 2017 - 10:00:01 PDT
