> On Jun 1, 2015, at 7:01 PM, Julio Dominguez <acheron24.hotmail.com> 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?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 01 2015 - 18:30:03 PDT
