Hi,
Can you check through some of the _MMPBSA_ptraj*.out files and see if any
errors were printed in those files as well as the _MMPBSA_*mdout files.
On Sun, Apr 10, 2011 at 9:16 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> Hello,
>
> using the serial version of MMPBSA.py i got the following error.
>
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> ptraj found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
> sander found! Using
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sandersander found!
> Using /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
>
> Preparing trajectories with ptraj...
> Preparing trajectories with ptraj...
>
> Preparing trajectories with ptraj...
>
> Preparing trajectories with ptraj...
> Preparing trajectories with ptraj...
>
> Preparing trajectories with ptraj...
> Preparing trajectories with ptraj...mv: `_MMPBSA_dummycomplex.inpcrd.1' and
> `_MMPBSA_dummycomplex.inpcrd' are the same file
> mv: cannot stat `_MMPBSA_dummyreceptor.inpcrd.1': No such file or
> directory300 frames were read in and processed by ptraj for use in
> calculation.
> Starting calculations...
>
> Starting gb calculation...
>
> calculating ligand contribution...
> mv: cannot stat `_MMPBSA_dummyligand.inpcrd.1': No such file or directory
> 300 frames were read in and processed by ptraj for use in calculation.
>
> Starting calculations...
>
> Starting gb calculation...
>
> calculating ligand contribution...
> 300 frames were read in and processed by ptraj for use in calculation.
> calculating ligand contribution...
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.Error! Ptraj failed. Check
> coordinate
> and topology files for the complex.300 frames were read in and processed by
> ptraj for use in calculation.
>
> Starting calculations...
>
> Starting gb calculation...
>
> calculating ligand contribution...
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
> Error! Ptraj failed. Check coordinate and topology files for the
> complex.NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
> calculating receptor contribution...
> calculating receptor contribution...
> calculating receptor contribution...
> calculating receptor contribution... calculating complex contribution...
> calculating complex contribution... calculating complex contribution...
> calculating complex contribution...
> Starting pb calculation...
>
> calculating ligand contribution...
> Starting pb calculation...
>
> calculating ligand contribution...
> Starting pb calculation...
>
> calculating ligand contribution...
> Starting pb calculation...
>
> calculating ligand contribution...
> calculating receptor contribution...
>
> calculating receptor contribution...
> calculating complex contribution...
>
> Calculations complete. Writing output file(s)...
>
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -5060.4993 EGB =
> -14223.5294NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
> calculating receptor contribution...
> calculating receptor contribution...
> calculating complex contribution...
> calculating complex contribution...
> calculating complex contribution...
>
> Calculations complete. Writing output file(s)...
>
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -5060.4993 EGB =
> -14223.5294NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
>
> Calculations complete. Writing output file(s)...
>
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -5060.4993 EGB =
> -14223.5294NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
>
> Calculations complete. Writing output file(s)...
>
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -5060.4993 EGB =
> -14223.5294NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py --clean to erase these files.
>
>
> Can anyone suggest me a solution to this.
>
> Regards,
> Vani
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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 Mon Apr 11 2011 - 06:30:03 PDT
