[gmx-users] a second defaults directive

Taeho Kim taeho.kim at utoronto.ca
Tue Aug 27 21:15:22 CEST 2002

Dear All,
Thank you for your help in advance.
When running grompp for energy minimization, what causes this error below?
grompp -f em -c dppc.gro -p dppc.top -o dppc
Fatal error: Found a second defaults directive, file "lipid.itp", line 9.  
The lipid.itp file: ( .top, lipid.itp, dppc.itp from Dr. Peter Tielemanhttp://moose.bio.ucalgary.ca/.)

What does the number  "[defaults]  /  1   1" mean?  Is it still valid with " [defaults] of nothing" in the lipid.itp file? 
;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS
;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et
;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are
;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,
;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as
;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS. 

[ defaults ]
1       1

[ atomtypes ]
;name     mass     charge ptype  c6           c12
   LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
  LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
  LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
   LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
  LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
  LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
   LP    30.9738    0.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
  LOS    15.9994    0.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS
  LP2    14.0270    0.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ
  LP3    15.0350    0.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ
  LC3    15.0350    0.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
  LC2    14.0270    0.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS

[ nonbond_params ]
~ ~  
Taeho Kim
Dept. of Chemical Engineering and Applied Chemistry 
Institute of Biomaterials and Biomedical Engineering 
University of Toronto
taeho.kim at utoronto.ca

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