Dear amber users,
I am confused in the different syntax available.
1. In the amber12 tools, as I am using amber12, acceptormask and donormask are the keywords BUT in tutorial they are mentioned as acceptor mask and donor mask. So which one is correct?
2. To refer a particular atom, like required in case of disulphide bond, I used :GLN.OE1 BUT in tutorial it has been mentioned as :GLN.OE1. So which one is correct?
3. Third query is most naïve. I know that in Hbond the donor is hydrogen bound to electronegative atom and acceptor is a electronegative atom present at different location. However, I don't see any Hydrogen in donor mask section and observe hydrogen mentioned in acceptor mask section.
donor mask :GLN.OE1
donor mask :GLN.NE2
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
Also what is the significance of the order by which atoms are represented in acceptor mask section?
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 18 2014 - 13:00:03 PDT
