Hi Asfa
In order to change the pb input: Go $AMBERHOME/src/mmpbsa_py
Use your favorite editor and open up utils.py.
Search for the string: *def pbmdin_old*
You should see the following:
&cntrl
ntb=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, cutcap=-1, xcap=0,
ycap=0, zcap=0, idecomp=0, ntpr=1,
ivcap=0, ntmin=2, igb=10, """)
you need to remove the following variables: *cutcap*, *xcap*, *ycap*, and *
zcap*
Save the changes and copy the file utils.py to the $AMBERHOME bin
directory..
NOTE: if you don't have write permissions use the {-use-mdins} option
On Thu, Jul 1, 2010 at 1:01 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> There are two central K+ ions which are essential and should be retained.
> I
> am using sander and explicit solvent method for running the simulations
> (even in the mmpbsa tutorial, sander is used
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm, I don't know
> how to use GB during MD runs).
>
> Regarding the correction you mentioned for the pb errors in utils.py, I'm
> too ignorant to do it.
>
> Can you plz suggest any other way out? I was following the tutorial since I
> have the latest Ambertools and Amber9 package but I'm ending with errors.
>
> On the other hand I tried to do mm_pbsa.pl in Amber9. There it's showing:
>
> Died at /soft/amber9//src/mm_pbsa/mm_pbsa_calceneent.pm line 498, <PDB>
> line
> 718.
>
> Can you plz tell me the radius of K+ ion so that I can add it in the*
> mm_pbsa_calceneent.pm file.
> Plz help.
>
> Thanx a lot...
> Asfa.
>
> *
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Thu Jul 01 2010 - 07:30:04 PDT
