Re: [AMBER] ionic strength conversion between and PBSA

From: Vlad Cojocaru <>
Date: Fri, 25 Oct 2013 17:44:53 +0200

Yes, you are right.. when using sander it is conerted to 100 ...

However, another strange thing I noticed is: when using mmpbsa_py_energy
if I change the 0.1 value in _MMPBSA_pb.mdin to 100 ... In the mdout it
appears 100000 ...
So, it looks like even if in the _MMPBSA_pb.mdin the value is in M, the
calculation is still done in mM .... It does the right thing after all
but its quite hard to follow ...

Well, I guess looking at the mmpsba_py_energy code should help ...


On 10/25/2013 05:08 PM, Jason Swails wrote:
> On Fri, Oct 25, 2013 at 10:21 AM, Vlad Cojocaru <
>> wrote:
>> Dear all,
>> I set istrng=0.1 in MMPBSA input (0.1 M accoring to the AmberTools 13.0
>> manual). According to the manual, PBSA uses mM as units .. Therefore in
>> the PBSA input file created by I should see istrng = 100 ...
>> However, in file _MMPBSA_pb.mdin I don't see this and istrng = 0.1 as in
>> my
>> This is either a bug or some information is wrong in the manual or I am
>> missing something.
>> My AMBER tree is fully updated since last night.
> I believe you are right when uses mmpbsa_py_energy to calculate
> the energy. If you set use_sander=1 in the &general section, does the
> resulting input file give the expected istrng?
> Thanks for the report!
> Jason

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Fri Oct 25 2013 - 09:00:06 PDT
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