Many thanks for this. Much appreciated.
Thank you for the reference too. This is also great help.
Have a good day
George
On Apr 24, 2012, at 9:03 PM, InSuk Joung wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best,
> InSuk Joung
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Received on Tue Apr 24 2012 - 13:00:04 PDT
