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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 16 2012 - 10:30:04 PDT
