Hi,
My name is Filip and i am using your product, Discovery Studio ver. 4.1. I am having some problems with specific protocols. I am trying to "Calculate Protein Ionisation and Residue pKa" on the exsample file given in the tutorial (file name: 2lzt.dsv)
As in the tutorial, i have removed water and NO3 molecules, applyed CHARMm forcefield, set dielectric constant to 11, and protonate protein at pH 5.5. Than i ran the protocol, - it ended with error (the picture of the job is, together with the log, compressed in the attached zip file - DS_problem.7z)
When running the protocol in debugging mode in Pipeline, no specific error is found.
I am following the protocol/tutorial found on this site: https://isp.ncifcrf.gov/files/isp/uploads/2010/07/Calculating-Protein-Ionization-and-Residue-pK.pdf
Overall some calculations like solvation, minimisation, calculate energy work, however beside "calculate protein ionisation and residue pKa" there are also others that don't work (for exsample: calculate eletrostatic potential - DelPhi failed).
Since the exsample file does not work, i am sure there is something wrong with the program.
If you need additional other information, please tell.
Filip
My name is Filip and i am using your product, Discovery Studio ver. 4.1. I am having some problems with specific protocols. I am trying to "Calculate Protein Ionisation and Residue pKa" on the exsample file given in the tutorial (file name: 2lzt.dsv)
As in the tutorial, i have removed water and NO3 molecules, applyed CHARMm forcefield, set dielectric constant to 11, and protonate protein at pH 5.5. Than i ran the protocol, - it ended with error (the picture of the job is, together with the log, compressed in the attached zip file - DS_problem.7z)
When running the protocol in debugging mode in Pipeline, no specific error is found.
I am following the protocol/tutorial found on this site: https://isp.ncifcrf.gov/files/isp/uploads/2010/07/Calculating-Protein-Ionization-and-Residue-pK.pdf
Overall some calculations like solvation, minimisation, calculate energy work, however beside "calculate protein ionisation and residue pKa" there are also others that don't work (for exsample: calculate eletrostatic potential - DelPhi failed).
Since the exsample file does not work, i am sure there is something wrong with the program.
If you need additional other information, please tell.
Filip
