Dear xplor mailinglist. My name is Yoanes Maria Vianney from UGhent. I want to calculate a 30-nt DNA-testosterone complex structure. For that I have prepared the basic files (PDB, psf, par, restraints, etc) and start to calculate by DGSA using the start_structures.py script. However, in the beginning of the calculation, there is a message in the log file showing
AT_Build::buildNode: cycle link found between atoms 31 LIG C4 and
31 LIG C3
removing bond.
AT_Build::buildNode: cycle link found between atoms 31 LIG C9 and
31 LIG C10
removing bond.
AT_Build::buildNode: cycle link found between atoms 31 LIG C14 and
31 LIG C8
removing bond.
AT_Build::buildNode: cycle link found between atoms 31 LIG C17 and
31 LIG C13
removing bond.
As such, the testosterone is not in a proper aliphatic ring anymore.
Attached to this email is the start_structures.py script. I am sorry for my
last email that I forgot to attach it.
What is the problem and what can be modified to prevent the breakage of the
bond here?
(e.g., we have
try:
with open('../LIG.psf', 'r') as fh:
dyn.breakAllBondsIn("not resname LIG")
In the IVM but it still remove the bond in the LIG.
Thank you in advance.
Best regards,
Yoanes Maria Vianney
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
start_structures.py
Description: start_structures.py
