I just have a questions about the output of the script. I have a implicit solvent trayectory of 1fs timestep, so I commented the water H-bond part, and I changed the coor hbond setup as follows:
coor hbond verbose select type HN .or. type O end select type HN .or. type O end -
first 51 nunit 1 begin 100 skip 100 stop 200000
Part of the output is :
READING TRAJECTORY FROM UNIT 51
NUMBER OF COORDINATE SETS IN FILE: 2000
NUMBER OF PREVIOUS DYNAMICS STEPS: 100
FREQUENCY FOR SAVING COORDINATES: 100
NUMBER OF STEPS FOR CREATION RUN: 200000
I-atom J-atom (Bridge) Lifetime Endtime
PROT 37 LYS HN - PROT 33 ALA O 0.60 1.00
PROT 43 LYS O - PROT 46 ALA HN 0.20 1.10
PROT 51 LEU HN - PROT 51 LEU O 0.20 0.40
I am not sure of understanding the 'lifetime' and 'endtime'. I saved structures every 100. I interpret the first line hbond (37-33) as existing during the time window 0.4-1.0, and in the second case (43-46) during 0.90-1.10, Is that correct?? I also noted cases as the third line were a Hbond is considered beetween C and N of the same residue. I read that one can define CUTHA = 180 to allow only linear Hbonds, nevertheless, the angles of the first structure (showed earlier in the output) range from 170 to 90 degrees, being the average angle ~160. How can i avoid strange angles without being too restrictive?
Last edited by Leonardo; 04/23/05 02:09 AM.