[AMBER] Suggestions on crossing energy barrier to break strong HBs

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Sat, 30 Jan 2021 05:10:35 +0530


I am simulating a protein system in which a heme molecule is strongly
hydrogen bonded (via 2 HB's) to one of the protein residues. These HB's are
expected to break during the course (around ~700 ns) of NPT run and shall
lead to the further cascade of bond breaking/making in the protein.

But, I do not see this initial breaking of HB's in my simulation. The run
parameters I am using are as follows

  imin = 0, irest = 1, ntx = 7, ntb = 2,
  pres0 = 1.0, ntp = 1, taup = 0.5, gamma_ln = 1.0,
  cut = 8.0, ntr = 0, ntc = 2, ntf = 2,
  tempi = 298.0, temp0 = 298.0, ntt = 3

May I please get some suggestions about what changes can be tried in the
simulation, so that the system could cross the energy barrier needed to
initiate the breaking of these HBs between protein residue and heme

Thank You,



*Please consider the environment before printing this email.*
information contained in this electronic message and any *attachments to 
this message are intended for the exclusive use of addressee(s) and may 
contain proprietary, confidential or privileged information. If you are not 
the intended recipient, you should not disseminate, distribute **or copy 
this e-mail. Please notify the
sender immediately and destroy all copies of 
this message and any attachments.***
**WARNING***: The recipient should 
check this email and any attachments for
the presence of viruses. JMI 
accepts no liability for any damage caused by any
virus transmitted by this 
AMBER mailing list
Received on Fri Jan 29 2021 - 16:00:02 PST
Custom Search