AMBER Archive (2002)

Subject: Linmin question...

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Thu Nov 14 2002 - 12:13:01 CST

 Dear Amber Users,

 I would like to know how Amber program deals with LINMIN
problems because I had a message during the minimization
procedure:

&cntrl
  ntr = 1, ntb = 2,
  ntc = 2, ntf = 2,
  ntp = 1, cut = 12.0,
  igb = 0, imin = 1,
  maxcyc = 3000,
  ncyc = 1000, ntmin = 1,
  dx0 = 0.1, dxm = 0.5, drms = 0.0001,
 &end
Hold the DNA fixed
200.0
RES 1 20
END
END

NSTEP ENERGY RMS GMAX
NAME NUMBER
   1000 -3.9389E+04 1.5778E+01 4.9878E+01
O 966

 BOND = 21.7094 ANGLE = 271.1805 DIHED
  = 371.0223
 VDWAALS = 3611.3175 EEL = -43662.7060 HBOND
  = 0.0000
 1-4 VDW = 215.3127 1-4 EEL = -323.9397
RESTRAINT = 106.8195
 EAMBER = -39496.1033

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP ENERGY RMS GMAX
NAME NUMBER
   1050 -3.9389E+04 1.5778E+01 4.9878E+01
O 966

 BOND = 21.7094 ANGLE = 271.1805 DIHED
  = 371.0223
 VDWAALS = 3611.3172 EEL = -43662.7047 HBOND
  = 0.0000
 1-4 VDW = 215.3127 1-4 EEL = -323.9397
RESTRAINT = 106.8196
 EAMBER = -39496.1023

     .... RESTARTED DUE TO LINMIN FAILURE ...

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX
NAME NUMBER
   1114 -3.9389E+04 1.5778E+01 4.9878E+01
O 966

 BOND = 21.7094 ANGLE = 271.1805 DIHED
  = 371.0223
 VDWAALS = 3611.3164 EEL = -43662.7028 HBOND
  = 0.0000
 1-4 VDW = 215.3127 1-4 EEL = -323.9396
RESTRAINT = 106.8196
 EAMBER = -39496.1012

     ***** REPEATED LINMIN FAILURE *****

 I made the same procedure as specified above before with a
different value on the DNA restriction (500)but I did have
no problem. I so in the manual and the FAQ although I did
not understand it very well.
 Thank you very much,

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

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