[gmx-users] grompp error : Atomtype HC not found

[Atila Petrosian]

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