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I gave that a try, and ran into trouble also. The generate_1KDF.inp script needs coordinate_infile="1KDF_mod" which doesn't seem to exist anywhere in the tree. Maybe it is supposed to be created from 1KDF.pdb, but that didn't happen following the tutorial instructions. If yo don't get generate to produce the .mtf, then nothing else is going to work right. The file that you need to edit and run is given as changeScritpsDir.sh, but the file is actually changeScriptsDir.sh -- pretty obvious I guess but it suggests the tutorial wasn't carefully tested by copying and pasting the commands into a shell. good luck, eab On 09/16/2016 06:34 PM, Hammond, Robert Glenn wrote: > Hi, > > > Thanks for the advice about the how to source using ".csh". > > > My main goal is to minimize my structure using CNS with water. I have come across this protocol with RECOORD scripts <http://nmr.chem.uu.nl/~abonvin/tutorials/Structcalc-Data/tutorial.html> but it is not outputting the files I need. The scripts are executed and files such as "OUTPUT_refinelong_*.gz" and 'hist_patches" are generated when I use the BRSV-G example data but it has been unable to output a topology file (.mtf) or a .pdb file whenever I use my .pdb file or any of the test data in the Structcalc-Data directory (1KDF or BRSV-G). > > > Overall, I have recently solved an NMR structure using CYANA and would like to minimize it with water using CNS. I have converted all of the necessary files ( .pdb, . upl, and .aco files) to the .tbl format as directed here <http://www.nmr2.buffalo.edu/nesg.wiki/Structure_Refinement_Using_CNS_Energy_Minimization_With_Explicit_Water> . However I am not sure if these RECOORDscripts work or if there is a better water refinement protocol available. Does anyone have a better protocol or any suggestions on how to use this one? > > > Regards, > > Robert Hammond