AMBER Archive (2005)

Subject: AMBER: problem with gb md

From: emilia wu (emiliawu_at_dicp.ac.cn)
Date: Thu May 05 2005 - 21:05:00 CDT

Dear AMBER users,

i am ruuning an MD with implicit solvent (igb=1) .first, i want to relax my system ,and my input file are shown below.

===========================================
pep:initial minimization prior to MD GB model
 &cntrl
  imin=1,
  maxcyc=500,
  ncyc=250,
  ntb=0,
  igb=1,
  cut=12
 /
===========================================
then,i input "sander -O -i pep_init_min.in -o pep_init_min.out -c pep.crd -p pep.top -r pep_init_min.rst",and i got the output file in 1 minute. i found something is wrong with the energy in the output file,and i copied here.

======================================================================
                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 nan nan 0.0000E+00 C34 1

 BOND = 199.1390 ANGLE = 606.5759 DIHED = 2318.4901
 VDWAALS = 134604.7930 EEL = -18304.6508 EGB = nan
 1-4 VDW = 1344.4585 1-4 EEL = 11078.6900 RESTRAINT = 0.0000
==========================================================================
here i attached my input,output,crd,and top files.


thanks in advance for any help !
emilia





                                 

　　　　　　　　emilia wu
　　　　　　　　emiliawu_at_dicp.ac.cn
　　　　　　　　　　2005-05-06

  • application/octet-stream attachment: gbmd.rar

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