Re: [AMBER] Error in preparing system using AmberTools19

From: Bill Ross <>
Date: Tue, 23 Jul 2019 00:18:35 -0700

Oops, I didn't read the obvious:

Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6
normal usage set)
Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)

Try 'list' in leap, and see if Na+ is defined. If not, it's because a
lib file isn't being loaded, e.g. because
dat/leap/parm/frcmod.ionsjc_tip3p is just params and not the model
itself. Your mission is to figure out what that lib should be, since
ions94.lib isn't current.


On 7/23/19 12:13 AM, Bill Ross wrote:
> Have you verified that leaprc.water.tip3p contains or sources ion
> parameters? By design, it shouldn't, which would likely explain your error.
>> I have not loaded ions94.lib this time and
>> loadamberparams frcmod.ionsjc_tip3p because they are taken care by source
>> leaprc.water.tip3p,
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Received on Tue Jul 23 2019 - 00:30:03 PDT
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