On Fri, May 17, 2024, Ramírez, Gustavo via AMBER wrote:
>
>I'm having some issues every time I try to add ions to my system that are
>different from Na+, K+, and Cl-. For some reason, *frcmod.ionsjc_tip3p* is
>not allowing me to use Br- and I-. Here I attached the script that I am
>using and the error screen.
>
>source leaprc.gaff2
>source leaprc.water.tip3p
>loadamberparams frcmod.mon
>loadoff monomer.lib
>
>loadoff atomic_ions.lib
>loadamberparams frcmod.ionsjc_tip3p
You should not use the two commands above: they are already included
in the leaprc.water.tip3p command, which contains the ion parameters
recommended for use with tip3p. (It's *possible* that loading all this
twice is causing a problem -- see below for debugging.)
>addIons2 MOL Na+ 2
>addIons2 MOL Br- 2
>addIons2 MOL Cl- 0
Unfortunately, your screenshot doesn't indicate anything about which of the
above commands led to the error. Run tleap interactively, and type in the
above commands to see where the error is coming from.
Also, please follow the suggestions in the error message: use the "list"
command to make sure that the ions you want are actually loaded. Use the
"desc" command to make sure that the offending residue name indeed refers to
the ion you want.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 17 2024 - 12:00:02 PDT
