Dear Jason,
thank you for the explanation; but with different values for surften (or
cavity_surften), I also obtain differen results, my question regards the
surfoff (or cavity_offset) parameter. If I re-run MMPBSA.py on the same
trajectory with different values for surfoff (or cavity_offset), the
DELTA G solv component, and also the DELTA G binding result, are
maintained, is it correct?
Federica
Il 16/10/2012 19:01, Jason Swails ha scritto:
> On Tue, Oct 16, 2012 at 11:58 AM, Federica Chiappori <
> federica.chiappori.itb.cnr.it> wrote:
>
>> Dear all,
>> I would like to report some**inconsistencies between the Amber (11 and
>> 12) manual and MMPBSA.py tool:
>> - default value of parameter /dielc/ is 1.0 in the manual and 4.0 in
>> MMPBSA.py
>>
> This appears to be true, but only affects normal mode analyses in vacuum
> (in GB, this value is ignored). I will adjust this to match the NAB
> defaults as well as the manual. IIRC, this is a left-over from the days of
> using the nmode program. (Another inconsistency is that dielc appears to
> be a simple dielectric rather than a distance-dependent dielectric like the
> manual claims).
>
> I will post an erratum.
>
>
>> - default value of parameter /drms /is 0.0001 in the manual and 0.001 in
>> MMBPSA.py
>>
> No, the default is correctly reported as 0.001 in the manual (p. 260).
>
>
>> Are the /surfoff /and /cavity_offset/ parameters employed during the
>> MMPBSA.py calculation?
>> I try different values for these parameters and the results are always
>> the same.
>> Moreover, I search these parameters in MMPBSA.py tool and they seems not
>> employed, is it possible?
>>
> They are passed to either mmpbsa_py_energy or sander as parameters to the
> PBSA program. The direct scaling of nonpolar energies is not done by
> MMPBSA.py.
>
> These values should only affect the ENPOLAR energies as reported by
> MMPBSA.py. When I ran MMPBSA.py with cavity_surften set to the default and
> again with cavity_surften set to 1.0, I got the following diffs:
>
> 40c40
> < ENPOLAR 51861.8683 84.3125
> 59.6179
> ---
>> ENPOLAR 1959.8310 3.1870
> 2.2536
> 43c43
> < G solv 48692.6780 77.3530
> 54.6968
> ---
>> G solv -1209.3594 3.7725
> 2.6676
> 45c45
> < TOTAL 29563.1241 123.7142
> 87.4792
> ---
>> TOTAL -20338.9133 42.5888
> 30.1148
> 54c54
> < ENPOLAR 51667.2433 91.3125
> 64.5677
> ---
>> ENPOLAR 1952.4741 3.4516
> 2.4406
>
> ...etc. So for me, the ENPOLAR energies are clearly changing, as they
> should. (Note, you cannot simply change 'cavity_surften' and use
> -rewrite-output, the calculations need to be re-run).
>
> HTH,
> Jason
>
--
_____________________________________________________________
Federica Chiappori, Ph.D.
Istituto di Tecnologie Biomediche - CNR
Via F.lli Cervi, 93
20090 Segrate (MI)
Phone: +39 02 26422606
E-mail: federica.chiappori.itb.cnr.it
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Received on Wed Oct 17 2012 - 02:30:04 PDT
