Re: [AMBER] Bug or feature of tleap

From: Jason Swails <>
Date: Mon, 1 Jun 2015 21:06:27 -0400

> On Jun 1, 2015, at 7:01 PM, Julio Dominguez <> wrote:
> Good day everyone,
> I was following the AMBER Advanced Tutorial 20 Metal Ion Modeling Tutorial, the 12-6 Lennard-Jones (LJ) Nonbonded Model. Now my problem arose by using the suggested input for tleap:
> source leaprc.ff12SB #Source the ff12SB force fieldloadoff atomic_ions.lib #Load the library for atomic ions

This is not necessary. leaprc.ff12SB automatically loads atomic_ions.lib. Loading it twice shouldn’t hurt, but it is already loaded automatically by the force field.

> mol = loadpdb 4V2Y_clean_A_2.pdb #Load the PDB fileloadamberparams frcmod.ionslrcm_cm_spce#Load the frcmod file for divalent metal ionsloadamberparams frcmod.ionsjc_spce #Load the frcmod file for monovalent metal ionssolvatebox mol SPCBOX 8 #Solvate the system using SPC water boxloadamberparams frcmod.spce #Load the frcmod file for SPCE wateraddions mol CL 0 #Neutralize the system using Cl- ionssavepdb mol Zn_4V2Y.pdb #Save the pdb filesaveamberparm mol Zn_4V2Y.prmtop Zn_4V2Y.inpcrd #Save the topology and coordiante filesquit #Quit tleap
> The interesting part is:If I have a atomic_ions.lib tleap loads it BEFORE it is called by the script.

What does this mean? Did you name one of your files “atomic_ions.lib”, or are you using the one inside $AMBERHOME/dat/leap/lib? The atomic_ions.lib file inside $AMBERHOME/dat/leap/lib is the standard template for all of the ions supported “natively” by tleap. If you name your own file “atomic_ions.lib”, then leaprc.ff12SB will load your “atomic_ions.lib” file *instead* of the one inside $AMBERHOME/dat/leap/lib. As a result, it may be that not all of the ions that should have been loaded actually were.

Could this be what is happening?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 01 2015 - 18:30:03 PDT
Custom Search