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Hello Gary-- > > 1.how do you write mixed python c /fortran based potentials using pypot? > Specifically I wanted to use c for calculating energies and derivatives but > python for all other set-up house keeping etc Probably the closest example to what you want to do is python/h3JNCPot.py in recent distributions. Depending on the nature of the numerical calculations, builtin Xplor-NIH or numpy code might be fast enough. If not, you'll have to go through swig. > 2. how can I access the non bonded list from c or fortran and from > python? There is no easy way to do this. Our experience is that all nonbond lists are different- different update frequency, distance cutoff, etc. We just roll our own when necessary. An example can be found in xplor/nmrPot/nbTargetPot.cc > 3. in PyPot based potentials is calcEnergy guaranteed to be called before > calcEnergyAndDerivs as shown in the example you give in the documentation > No. calcEnergy *can* be called separately (for instance, in Monte Carlo algorithms) so that expensive gradient calculations aren't made, calcEnergyAndDerivs must return an energy. One option is for calcEnergyAndDerivs to call calcEnergy. I hope this helps-- Charles
--
Charles Schwieters email: Charles <at> Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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Hello Mehdi-- > > Are Sparky output files compatible with Xplor NIH for automated NOE > assignement with PASD/MArvin facility? Not currently. The supported formats are nmrdraw, nmrstar, pipp and xeasy. You have the option of converting to one of the supported formats or working with me to write an nmrstar reader. best regards-- Charles
--
Charles Schwieters email: Charles <at> Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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Hello Mehdi-- > > Thank you for your reply; Actually one of output options of SPARKY is XEASY > format, how can I convert the xeasy format (chemical shift list and peak > list) to the readable format by XPLOR or PASD?MARVIN facility? > xeasy should be directly readble by PASD. In your initMatch TCL script, place a package require xeasy at the top and then use process3dXeasyPeakTable Shift tables must be in nmrstar or pipp format. If there is an xeasy shift format I will gladly add that. best regards-- Charles
--
Charles Schwieters email: Charles <at> Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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Hello Mehdi-- > > I applied the modification you mentioned in last email, I also converted the > XEASY shift list (.prot file) to pipp by dataconverter on BMRB site, however > when I run the script "initMatch TCL" there is error message: > > "Missing required flag -fromHeavyatomColumnName > Neither -pot nor -shiftAssignments defined in call to > recordUnfoldedPositions" > These messages indicate that arguments to the function calls are missing. If you send me your script, I think I can fix things up. best regards-- Charles
--
Charles Schwieters email: Charles <at> Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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Dear All, At present I have generated pdb, psf and par for PRE docking using spin labels in 6 positions with four orientations for each. I have recently attempted to utilise the same script for generation of the above files for 9 spin labels. However, when I do so I am presented with a parameter error, such that it cannot find a specific atom of 7th spin label and therefore xplor terminates. I have not encountered this error before using 6 positions and all I have done is to increase the total number of spin labels and included the relevant mutation sites for xplor to read. Is it possible that xplor cannot handle too many i.e. > 24 spin labelled positions due to the number of coordinates being read in and created at one time? I have further tried using 7 spin labels and I am presented with the same error. Many Thanks and Kind Regards Simon Skinner -- -- Simon P Skinner Protein Chemistry Group Leiden Institute of Chemistry, Universiteit Leiden Phone: +31 71 527 6089 / Fax: +31 71 527 4349 E-mail : skinnersp <at> chem.leidenuniv.nl
Hello Simon-- > > At present I have generated pdb, psf and par for PRE docking using spin > labels in 6 positions with four orientations for each. I have recently > attempted to utilise the same script for generation of the above files > for 9 spin labels. However, when I do so I am presented with a > parameter error, such that it cannot find a specific atom of 7th spin > label and therefore xplor terminates. I have not encountered this error > before using 6 positions and all I have done is to increase the total > number of spin labels and included the relevant mutation sites for xplor > to read. Is it possible that xplor cannot handle too many i.e. > 24 > spin labelled positions due to the number of coordinates being read in > and created at one time? I have further tried using 7 spin labels and I > am presented with the same error. > Please send the error output, and we should get to the bottom of this issue quickly. I modified eginput/pre/refine/generate.py in the Xplor-NIH distribution to generate 9 tags, and that worked just fine. best regards-- Charles
--
Charles Schwieters email: Charles <at> Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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