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Hello Indra-- > I am trying to add MTSL paramagnetic probe in a membrane protein > using xplor. > I modified the addAtoms.py file with my protein sequence and my > original structure (start.pdb) at proper places. I used CYSP as the > MTSL probe at the desired position (as suggested in the tutorials) in > the protein sequence. When I executed the command "xplor -py > addAtoms.py" , it seems working and new.pdb and new.psf files are > generated with MTSL labeled at proper position in the protein > sequence. When I compare the new.pdb with start.pdb, it seems that > the structure is distorted (alpha helix to random coil). Of course, this should not happen. Are there any diagnostic messages? > I used > cysp.top and cysp.par as topology and parameter files. CYSP is now included in the standard toppar input, so these additional files should cause errors (with recent versions of Xplor-NIH). So there must be some error messages... best regards-- Charles - -- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAk4IlCUACgkQPK2zrJwS/lYZngCfeOD1xkUs3Re0LODVHTSxwhTF qOMAn1s00m731GqWJ7UxVDlwaHTHZBsa =xhNk -----END PGP SIGNATURE----- _______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
