> I manually corrected the following in the prmtop:
No one can answer questions based on that move. Best to fix your build
so that there is a supported prmtop.
Bill
On 10/12/17 8:27 AM, Sanaa ALAbbad wrote:
> 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 - 15:00:02 PDT
