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
>>
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>>
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Received on Sun Jul 01 2012 - 00:30:02 PDT
