[gmx-users] a second defaults directive

[David van der Spoel]

On Tue, 2002-08-27 at 21:15, Taeho Kim wrote:
> 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? 
> --------
tells you what nonbonded type to use and what combination rules (see
manual). Just throw out the one from lipids.itp


> ;; 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
> ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿà›î±ê왨¥Šx%ŠË`›î±êìþ
> 虧,þŠà†ÛiÿÿðÃஉšrÏè®æj)fjåŠËbú?‚lÿºÇ«°ù^jǝ¢í¦‹-þéÿ²æìr¸›z·ª¹ë-²Ú-
éb²ßÔ±ëa{0Š{^­öœzŠìzwb¶Ú ›î±êìþ·ª¹ë-þ
> 虧,þŠà
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++