AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS

From: Zhihong Yu <>
Date: Mon, 25 Sep 2006 11:03:28 +0800

Dear All,

        As general MD procedures, I've finished the "Minimisation Stage 1 - Holding the solute fixed" and got a "relaxwater_min.rst" file, then I perform the "Minimisation Stage 2 - Minimising the entire system" based on this "relaxwater_min.rst", because I want to restrained all residues in 15~20 shell of an inhibitor.[the method is described in detail on the page 4575 in professor simmerling's paper(J. Med. Chem. 2006, 49, 4574-4580)] so I write mdin file as follow:

Hold the 15-20 A shell and relax others
  imin = 1, ncyc = 1000, maxcyc = 3000,
  ntb = 1, ntr = 1
Hold the 15~20A shell fixed part01
RES 144 160
.....(other 31 restrained parts are omitted here)
Hold the 15~20A shell fixed part33
ERS 521 525

my system include 27083 atoms, and I ran this minimisation by PMEMD version 9 on 8 nodes, after about 1 hours, the computation looks like to be choked, so I killed the job, checked the mdout file (attached as relaxsystem.out) and found out ".... RESTARTED DUE TO LINMIN FAILURE ...", I've searched this "LINMIN FAILURE" on this mail list and found that it's not a very serious problem. But after checking the mdout file, I found out another strange thing about the energy of "1-4 EEL" and "EAMBER", in many steps they were represented by "*************", I think it's just too big to display. Moreover, form the NSTEP of 150, the RMS increased to 5.2082E+10, it seems that these values were abnormal, whether it means our system have some serious problem? or my mdin file have some problem?

    Any advice will be greatly appreciated! Thanks in advance & Best regards!

    yours sincerely, Zhihong Yu

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Wed Sep 27 2006 - 06:07:09 PDT
Custom Search