You don't have to redo your MD, just redo your mmpbsa with the new
scripts that are more flexible. Let's start from there ...
Also, the radius problem in Amber9 was reported and resolved before on
the mailing list. You can google it in the archive.
Ray
On Sun, Jul 1, 2012 at 12:10 AM, <rajeevy.iitk.ac.in> wrote:
> Dear Ray,
> In latest AmberTool, I have to use mm_pbsa.pl or any other and also the
> radius of F is needed or not??
> If i use latest AmberTool for my calculations, all the minimization and
> equilibration that I did in Amber9, should be done again in latest
> version?
> Since I am new in this field and not know much, so
> If possible please let me know the whether I can use Amber9 for mm_pbsa.pl
> calculations and where I should use radius of F.
>
> With Regards
> Rajeev Yadav
>
>
>> I strongly suggest you try the latest AmberTools release for your project
>> ... It's free.
>>
>> Ray
>>
>> On Sat, Jun 30, 2012 at 3:36 AM, <rajeevy.iitk.ac.in> wrote:
>>
>>> Hi,
>>> There are three F atoms in my ligand and using mm_pbsa.pl for
>>> calculation
>>> in AMBER9. Can some one tell me how an where to set radius of F in
>>> MMPBSA
>>> calculation.
>>> It shows the error in the terminal window like this
>>> Died at /home/psen/AMBER9/amber9/src/mm_pbsa/mm_pbsa_calceneent.pm line
>>> 498, <PDB> line 9267.
>>> And in log file I got the following information:
>>> Calculating energy / entropy contributions
>>> Calc contrib for ./snapshot_com.crd.1
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Calc PBSA
>>> Generate PQR
>>> No radius found for F2 9265 in residue COU 584
>>> Thanking You
>>> with regards
>>> Rajeev Yadav
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>
>
>
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Received on Sun Jul 01 2012 - 08:00:04 PDT
