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Hello Alex-- > I tried to calculate the structures using the nucleic.top/nucleic.par files > and unfortunately the problem persists. I have also noticed that in my new > coordinate pdb file generated using the nucleic.top/nucleic.par files, the > position of the H41 and the H42 atoms is interchanged in some of my cytosine > residues. this is due to a missing improper entries in nucleic.top for CYT: IMPRoper N3 C4 N4 H42 IMPRoper C5 C4 H41 H42 IMPRoper N3 C4 H42 H41 This will be fixed in the next release. > I also went over my script and made sure that the NOE term was > indeed on and the force constant is reasonable. the only force field term which explicitly affects the chi angle would be in the DIHE energy term. Do you have this enabled? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFF4wbVPK2zrJwS/lYRAppNAJ97mqBtjS+3GVDsPEbNpQZ15F3txgCfQgsm Crzaiw0bO6TKRPa//Q0hyUc= =U/uK -----END PGP SIGNATURE-----
