[AMBER] Error reading Ruthenium complex residue

From: Sanaa ALAbbad <salabbad79.gmail.com>
Date: Thu, 12 Oct 2017 09:27:17 -0600

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)
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 - 08:30:01 PDT
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