The first error has been well-documented (Use of uninitialized value in
concatenation) in the archives, although I'm not sure a good solution has
ever been suggested. Regardless, the second error listed here might be the
main culprit and is fairly self-explanatory.
Prmtop ./pdb1k4u_apo2.prmtop and coord.file ./snapshot_com.crd.1 have
different atom numbers
This means that the atoms numbers you gave the input file when you extracted
coordinates were not consistent with the atom numbers in the complex
topology file you provided. You will need to go back and get that step
correct before the binding energy calculation will work and/or give you
useful information.
As a side note, MMPBSA.py has a mask guesser that helps determine that
receptor and ligand masks without the user being required to input atom
numbers to help avoid these types of mistakes.
I hope that helps.
-Bill
On Wed, Apr 6, 2011 at 7:18 AM, vani panguluri <vanipanguluri.gmail.com>wrote:
> hello,
>
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
> mm_pbsa_createinput.pm line 596.
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
> mm_pbsa_createinput.pm line 596.
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
> mm_pbsa_createinput.pm line 596.
> Prmtop ./pdb1k4u_apo2.prmtop and coord.file ./snapshot_com.crd.1
> have different atom numbers
> For details see:
>
> http://ambermd.org/Questions/mm_pbsa.html#check_atom_nr_prmtop_and_crd_differat
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
> mm_pbsa_calceneent.pm line 1137.
>
> can one check why i got this and how to solve it.
>
> Thanks & Regards,
> Vani
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Apr 06 2011 - 04:30:04 PDT
