Dear All,
I am working with a G-quadruplex system. I want to incorporate two
modifications in the G-quadruplex sequence at 9 and 24 position as DF
and BF respectively. When I first incorporated the modifications and ran
MD simulatIon, in the production stage, the modification and the
G-Quadruplex separated as if the modification is not a part of the
system. Now, I am using 'bond' command to make covalent bonds between
the atoms in the DNA backbone as follows :
bond mol.8.O3' mol.9.P
bond mol.9.O3' mol.10.P
bond mol.23.O3' mol.24.P
bond mol.24.O3' mol.25.P
But after running this command, the g-quadruplex is splitting into
multiple chains with TER before and after 9th and 24th modifications.
Presence of TER is the end of one chain. So what might be causing this.
Please provide insight and suggestions on how to correctify this.
Thank you in advance
Regards,
Priyasha
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 12 2023 - 05:00:02 PDT
