Re: [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+

From: InSuk Joung <>
Date: Tue, 24 Apr 2012 15:03:18 -0400

The correct way to load the force modification file is typing

loadamberparams frcmod.ionsjc_spce

as a command of leap.
Be careful that there are two other parameter files: frcmod.ionsjc_tip3p
and frcmod.ionsjc_tip4pew.
You need to choose one depending on the water model you use. The parameters
were optimized for SPC/E, TIP3P, and TIP4Pew water models, respectively.
See the reference for more details:

On Tue, Apr 24, 2012 at 1:59 PM, George Tzotzos <> wrote:

> I'm trying to create topology files for a constant pH simulation of a
> protein ligand complex.
> I've loaded: tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.constph
> I tried to neutralise the system by: addions COMPLEX Na+ 0 (5 ions added).
> When I tried to save the topology and coordinate files I've got "For atom:
> .R<Na+ 127>.A<Na+ 1> Could not find type: Na+"
> I checked the archive and found that the problem had been reported earlier
> (25 July 2010). The suggestion by Bill Ross was to find a load an
> appropriate "parm.dat (or frcmod)
> having the parameters for Na+ vdw". It was suggested that such file may be
> " in /amber10/dat/leap/parm/ since we see /amber10/dat/leap/parm/parm10.dat
> (or possibly in /amber10/dat/leap/lib/). With that in mind you might see a
> .dat or .frcmod file with a name including 'ion' - grep Na+ to determine if
> it is there and try loading that".
> One such file is frcmod.ionsjc_spce. I'm not sure if this is the right one
> for the purpose of my simulation.
> I tried to load it by: tleap -s -f
> $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce
> and got: syntax error.
> Any help on how to get round this problem is much appreciated
> Regards
> George
> _______________________________________________
> AMBER mailing list

InSuk Joung
AMBER mailing list
Received on Tue Apr 24 2012 - 12:30:02 PDT
Custom Search