AMBER Archive (2005)

Subject: AMBER: need clarification on EWALD BOMB error

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Thu Nov 17 2005 - 04:03:22 CST

dear amber friends,
i am doing 1ns dynamics for some set of protein molecules whose AA sequence
varies at only one position. i did dynamics for 7 molecules and got the
results successfully by same procedure. when i repeat the same procedure for
8th molecule it produces EWALD BOMP error in equilibration process. i
searched the previous quires in the amber reflector sites it say i have to
change the conditions slightly like in the following amber page
http://structbio.vanderbilt.edu/archives/amber-archive/2002/1120.php
i don't know, is it advisable to change the parameter for one calculation.
how much this parameter will affect the dynamics. please give some good
suggestion on this problem. i attached my output files also here for
equilibration process 

--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
  • application/octet-stream attachment: eq.out
----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu