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Hello Jie-rong-- I'm replying to the list, because it may help others. > > First, I tried to use (eginput/PSF_generation) addAtoms.py to add MTSL, but I > couldn't get a folded structure as shown in your example files. > > Here is some lines of pdb file I input > === > ATOM 16 HG1 MET 1 26.311 24.347 5.363 0 0 > ATOM 17 HG2 MET 1 25.43 25.902 5.514 0 0 > ATOM 18 HE1 MET 1 23.706 23.466 8.265 0 0 > ATOM 19 HE2 MET 1 25.427 23.475 7.749 0 0 > ATOM 20 HE3 MET 1 24.552 25.026 7.991 0 0 > ATOM 21 HY1 MET 1 28.543 23.329 2.359 0 0 > ATOM 22 HY2 MET 1 29.629 24.547 2.219 0 0 > ATOM 23 HY3 MET 1 28.842 23.995 0.893 0 0 > ATOM 24 N GLN 2 26.335 27.77 3.258 1 0 > ATOM 25 CA GLN 2 26.85 29.021 3.898 1 0 > ATOM 26 C GLN 2 26.1 29.253 5.202 1 0 > ATOM 27 O GLN 2 24.865 29.024 5.33 1 0 > ATOM 28 CB GLN 2 26.733 30.148 2.905 1 0 > ATOM 29 CG GLN 2 26.882 31.546 3.409 1 0 > ===== > > This proton-added file is generated from NAMD psfgen script, the main > difference comparing to example file is the final two columns (I think they > are size and charge). Is it the reason? If yes, how to generate a suitable > pdb file as xplor input? > Are you saying you can't get the addAtoms script to read a NAMD-generated pdb? It's had to say what's wrong without seeing the error messages. On the other hand if, in that script, you replace the addUnknownAtoms command with protocol.genExtendedStructure() a valid pdb will be created- but with an extended protein structure. > Second question is, how to use PRE information I have to calculate the > sturcture? Originally, I thought it would be like using NOE as distance > restraints and annealing protocol such as "sa.inp", but I also saw > "PMAGnetic" command in the manual...... Could you give me a hint, example > scripts, or point me to some tutorial files for this kind of calculation? Please see http://spin.niddk.nih.gov/clore/Software/pre_distribute.tar.Z for a full example. If you have further questions, please contact me. I do intend to include that example in the Xplor-NIH distribution at some point. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFHvxtIPK2zrJwS/lYRAspYAJsEM1eaxwGhp2rj3bRABREeFaFnkACfXFc/ 63tZqQW7+nvrf+tO1Ly3UB8= =OBch -----END PGP SIGNATURE-----
