| Hi all, I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. Renaming of POP to POPC in the .gro files doesn't matter... the main thing is to change the [Defaults] in the lipid.itp file (this eliminates the LC3 atomtype not found error) my .top files and modified lipid.itp files look like. --------------------------------------------------- grompp.top -------------- #include "ffgmx.itp" #include "lipid.itp" #include "popc.itp" #include "protein.top" #include "spin.top" #include "ions.itp" #ifdef FLEX_SPC ; removed these following lines from the protein.top file and appended into one single .top file. #include "flexspc.itp" #else #include "spc.itp" #endif #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif [ system ] ; name BR_103C [ molecules ] ; name number Protein 1 DRG 1 POPC 154 SOL 13393 --------------------------------------------------- lipid.itp (notice the defaults directive is commented out... this eliminates the AtomType 'LC3' not found error) --------- ;; 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 contd............... --------------------------------------------------- That is all the modifications required for running the simulation. Hope this helps people with similar problem in the future. Venks Venky Krishnamani Dr.Janos K. Lanyi Lab, D320, Medical Sciences D University of California, Irvine On May 29, 2006, at 12:23 PM, Arindam Ganguly wrote: Hi All, |
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