I forgot to cc the mailing list when I sent out the correction. It was a bad improper equilibrium value for N-terminal gly's Ca "chirality."
The fix is in parallhdg_procheck.pro, which I just updated in the CVS. --JK Begin forwarded message: > From: [email protected] > Date: Tue Aug 13, 2002 05:32:10 PM US/Eastern > To: [email protected] > Cc: [email protected] > Subject: TheGly problem in XPLOR 3.851 > > John, > > Family is ok but does not like it here as much as maryland as you can > imagine! > > Thanks for your prompt reply. When I was testing the program here, I > met a > problem with glycine at the very N-terminus. Basically, no structure > generated by sa.inp passes the accept.inp script. This was because of > the > bad angles of gly (only at the N-terminus according to my testing). > Here > are angle violations greater than 5 degrees from accept.out: > > (1 N | 1 CA | 1 C) 119.439 equil. 109.500 delta 9.939 energy 15.044 > const. > 500.00 > (1HA1 | 1CA | 1 C) 83.814 equil. 109.500 delta -25.686 energy 100.492 > const. 500.00 > ( 1HA2| 1 CA | 1 C) 120.373 equil. 109.500 delta 10.873 energy 18.008 > const. 500.00 > > This is also reflected in the impropers as you can expect. Due to this, > the total energy increases by 6 fold as compared to a control > calcualtion > when I place Gly elsewhere. Adding one more residue before Gly > immediately > led to an ensemble of structures (using an identical NOE list) with high > success rate (passing accept.inp). > > I'm wondering why. Thanks and if you need more details let me know. > But I > assume you may see this by setting a 10mer peptide calculation. > > Talk to you later! > > Gus > ________________________________ > Guangshun Wang, Ph.D. > Assistant Professor > Eppley Cancer Institute, Room 3018A > University of Nebraska Medical Center > 986805 Nebraska Medical Center > Omaha, NE 68198-6805 > > http://www.unmc.edu/Eppley/faculty/f_wang.html > >
