Hi Oliver,
On Thu, Apr 21, 2011 at 9:26 AM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Hi Jason,
> thanks for your help with my ligand setting problem.
> I got it, and I really did not realize that I strip the water out :o)
>
> Here's one thing I find strange with the MMPBSA.py script:
> When starting pure PB calculations using
>
> &pb
> sander_apbs=1, indi=1,
> /
>
> I get the start of the output
>
> ptraj found! Using /usr/local/amber11/bin/ptraj
> sander found! Using /usr/local/amber11/bin/sander
> sander.APBS found! Using /usr/local/amber11/bin/sander.APBS for PB
> calculations
> Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
> Yours are modified Bondi radii (mbondi)
>
Ah... This is really a non-issue. igb is set to 5 by default. I never put
in a switch to make sure that this check is only done if you're doing a GB
calculation. Therefore, you can just ignore this. This may be worth
releasing a patch for, but I think I may wait for the next (real) issue that
shows up. However, the GB defaults don't matter if you don't include a &gb
namelist, since GB calculations aren't even done.
>
> Preparing trajectories with ptraj...
> and so on
>
> with the Warning relating to GB calculations.
> As gbsa is set to 1 by default, I tried to switch that of by adding a
> section
>
> &gb
> gbsa=0
> /
>
> and to my surprise, the script starts doing GB calculation !?
>
Yes, that's a feature. If you include a namelist, that's interpreted as "I
want to do this type of calculation". I thought that was preferable to
having to set "pb = 1" or something within the &pb namelist for a PB
calculation. I thought this was documented in the manual, but I'll go back
and check again. Thus, for instance, if you want to do an alanine scanning
calculation, which only has 1 namelist variable, you need to set
&ala
/
In order to activate alanine scanning (if you don't need to change the
default of the 1 variable there). Note that the GBSA variable is the
Non-polar solvation free energy switch. If = 1, it uses LCPO to calculate
the surface area (and multiplied by surften to get the ESURF energy).
HTH,
Jason
> I hope that you can reproduce that issue.
>
> Best regards,
> Oliver
>
>
> --
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 21 2011 - 10:30:02 PDT
