Re: [AMBER] Error reading Ruthenium complex residue

From: Szymon Żaczek <>
Date: Thu, 12 Oct 2017 18:51:35 +0200

Dear Sanaa,

have you considered using 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: 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 <>:
> 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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Received on Thu Oct 12 2017 - 10:00:01 PDT
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