I don't think you need cutcap for typical mmpbsa calculations. It's
for Holger's "hybrid solvent" approach to mmpbsa ... it won't be used
even if you set it.
All the best,
Ray
On Wed, Nov 23, 2011 at 5:57 AM, Qinghua Liao <fantasticqhl.gmail.com> wrote:
> Dear Bill,
>
> Thanks very much for your explanations. Right now I got it. Thanks again.
>
>
> On Wed, Nov 23, 2011 at 2:13 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> Yes, you can set saltcon/istrng however you want. These two variables do
>> not change the results drastically, but the difference will depend on the
>> method you choose. You can see the actual dependence on salt concentration
>> by looking up the generalized born and poisson-boltzmann equations.
>>
>> -Bill
>>
>> On Wed, Nov 23, 2011 at 8:08 AM, Qinghua Liao <fantasticqhl.gmail.com
>> >wrote:
>>
>> > Dear Bill,
>> >
>> > Thanks very much for your fast reply. Do you mean that I can choose them
>> > freely according my purposes? However what are the differences of the
>> > binding free energy between 0.0 and 0.1 for the two items, respectively?
>> > Thanks very much!
>> >
>> >
>> > Best Regards,
>> >
>> > Qinghua
>> > Ph.D. student
>> > Juelich Research Center
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best Regards,
>
> Qinghua
> Ph.D. student
> Juelich Research Center
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Nov 23 2011 - 11:00:04 PST
