Dear All,
I have a very general question about running MD simulation for proteins. I know
that AMBER automatically assigns the Nterm and Cterm residues as NXXX and CXXX.
My question is in that whether in an MD, the charges on an uncapped Nterm or
Cterm can interact with the protein and bring about unusual distortions in the
structure ? In other words,
is it always necessary to cap the ends by say NME and ACE or AMBER does take
care of this issue internally ?
I would look forward to hear hear from you. Thanks a lot in advance.
Best Regards,
Moitrayee
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 14 2013 - 23:30:03 PDT
