Dear Justin, Thanks for answer. You said " There is no reason to use this totally obsolete force field (ffgmx.itp)". I used ffgmx.itp, because there was a example.top file in Tieleman's web site: ------------------------------------------------------- ; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion ; alm.itp can be made in a straightforward manner with pdb2gmx, starting ; with a pdb file of alamethicin. ; make sure lipid.itp, popc.itp and alm.itp are in a location where ; grompp can find them (GMXLIB, current directory, or directory given in ; the .mdp file with the include option. #include "ffgmx.itp" #include "lipid.itp" #include "popc.itp" #include "alm.itp" #include "ions.itp"
#ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Alm on surf + relaxed popc [ molecules ] ; name number Protein 1 POPC 128 SOL 3552 Na 1 ------------------------------------------------------- Based on your suggestion, I used following in my topology file (I deleted ffgmx.itp): #include "lipid.itp" #include "dppc.itp" #include "lig.itp" ------------------------------------------------------- But I encountered with: ------------------------------------------------------- Fatal error: Syntax error - File lipid.itp, line 11 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes ------------------------------------------------------- lipid.itp file from Tieleman's web site is as follows: ------------------------------------------------------- ;; 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 ------------------------------------------------------- How to resolve that? Best, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.