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Hello Jie-rong-- > To properly include solvent, you mean I should solvate the starting structure > and coordinate with water box or water sphere? What do you mean "an > appropriate" temperature? > room temperature, or whatever corresponds to your experiment. But let's forget about water for now, and concentrate on working with the given protocol. > I tried to run "saWithPreAll-3conf.py", however, came out some error > messages: > > The final few lines in the log file: > ################################### > %POWELL-ERR: Line search abandoned this is a normal message. > > The error from xterm window: > ############################ > Traceback (most recent call last): > File "<string>", line 2, in ? > File "/Users/huang/XplorNIH/xplornih2.19/python/trace.py", line 180, in run > exec cmd in dict, dict > File "<string>", line 1, in ? > File "saWithPreAll-3conf.py", line 1091, in ? > structLoopAction=structLoopAction).run() > File "/Users/huang/XplorNIH/xplornih2.19/python/simulationTools.py", line > 229, in run > s.structLoopAction(s) > File "saWithPreAll-3conf.py", line 942, in structLoopAction > en[xn] = XplorPot(xn).calcEnergy().energy > AttributeError: 'float' object has no attribute 'energy' this is due to one of the few incompatible changes in Xplor-NIH in the past few years. Please change calcEnergy().energy to simply calcEnergy() My apologies for this change. > Besides, some questions about the script: > The input coordinate: random3Alts1.pdb is not an extended protein. Will it > be > exteneded later in the script (and where it is stated) or I can also start > from extended file? Do you want it extended? If so, place a import protocol protocol.genExtendedStructure() after reading the coordinates. > > What is "setTaucAtoms" and what is clock atoms? I don't really understand, > could you explain a little bit more? These pseudo atoms represent the value of tau_c (correlation time). The positions can be varied to optimize this value. Please see http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/prePot.html > > In "def setConstraints(k_ang, k_imp)" part, is there any relation between > "nconf" and the number of "ALT"s (e.g. ALT1, ALT2...)? In > "random3Alts1.pdb", there are only ALT1, ALT2, and ALT3, but in the script, > its up to 10 ALTs (0 to 9)? Any reason? or it doesn't matter? The script can deal with up to 10 chomophore conformations, but there are only three in random3Alts1.pdb. > What's the > difference between "inter = (segid "ALT1") (segid "ALT1")" and "inter = > (segid " ") (segid "ALT1")"? > These constraints interaction statements are the most difficult aspect of the script, and should be changed very carefully. inter = (segid "ALT1") (segid "ALT1") specifies interactions of ALT1 with itself. inter = (segid " ") (segid "ALT1") specifies interactions between ALT1 and the DNA. Note that the ALTs (different configurations of the TED chromophore) should not interact with each other, and, thus, there are no constraints interaction statements with cross terms (e.g. ALT1 with ALT2). I hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIB3AuPK2zrJwS/lYRAnWaAKCIVrcVjobqtmGKVUJcfQ+qwUYsmACfUAjo ijK8I+wQYNopLwLLhXgHRC8= =oPYq -----END PGP SIGNATURE-----
