Re: [AMBER] Bug or feature of tleap

From: David A Case <>
Date: Mon, 1 Jun 2015 21:00:39 -0400

On Mon, Jun 01, 2015, Julio Dominguez wrote:

> 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 field
> loadoff atomic_ions.lib #Load the library for atomic ions

Note that leaprc.ff12SB (or better, leaprc.ff14SB) already has this command
in it. So the second line is redundant.

> mol = loadpdb 4V2Y_clean_A_2.pdb
> loadamberparams frcmod.ionslrcm_cm_spce
> loadamberparams frcmod.ionsjc_spce
> solvatebox mol SPCBOX 8
> loadamberparams frcmod.spce
> addions mol CL 0
> savepdb mol Zn_4V2Y.pdb #Save the pdb file
> saveamberparm mol Zn_4V2Y.prmtop Zn_4V2Y.inpcrd
> quit
> The interesting part is:If I have a atomic_ions.lib tleap loads it
> BEFORE it is called by the script. Besides, this loading somehow blocks
> the loading of frcmod.ionslrcm_cm_spce and the rest of parameters.

How do you know that this loading is blocked?

I cannot seem to reproduce this behavior. Try this:
before the addions step (which I assume is where the error arises), issue
a "list" command to see what units you have: is CL (etc.) present?

Also, please give the *exact* error message you get from the addions command.
This is much more useful information than just a report that a certain command

Changing the name to atomic_ions.bil will indeed keep the leaprc.ff12SB
script from finding and loading this file, but I don't see problems
with loading the file twice. What happens if you leave the name of the
atomic_ions file unchanged, but just remove second line of your script?


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Received on Mon Jun 01 2015 - 18:30:02 PDT
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