Hi,
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:
http://pubs.acs.org/doi/abs/10.1021/jp8001614
On Tue, Apr 24, 2012 at 1:59 PM, George Tzotzos <gtzotzos.me.com> 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
>
>
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>
--
Best,
InSuk Joung
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Received on Tue Apr 24 2012 - 12:30:02 PDT
