[gmx-users] errors with charmm36 ?

[Albert]

Hello:

I am trying to equilibrate a membrane system which contains both POPC 
and POPG. I generate the system with charmm-gui, and I try to minimize 
it in Gromacs. Here is  my em.mdp file:

define     = -DPOSRES_POPC  -DPOSRES_POPG
constraints     = none
integrator     = steep
dt         = 0.001
nsteps         = 50000
nstlist     = 1.0
ns_type     = grid
rlist         = 1.0
coulombtype     = PME
rcoulomb     = 1.0
vdwtype     = cutoff
rvdw         = 1.0
optimize_fft     = yes
emtol         = 800.0
emstep         = 0.01
pbc        = xyz
cutoff-scheme = Verlet

It said the following:

-----------------------------------------------------------------------------------------
WARNING 1 [file em.mdp, line 18]:
   Unknown left-hand 'define' in parameter file

Warning: atom name 3 in topol.top and merge.pdb does not match (C13 - H12A)
Warning: atom name 4 in topol.top and merge.pdb does not match (C14 - H12B)
Warning: atom name 5 in topol.top and merge.pdb does not match (C15 - C13)
Warning: atom name 6 in topol.top and merge.pdb does not match (H12A - H13A)
Warning: atom name 7 in topol.top and merge.pdb does not match (H12B - H13B)
Warning: atom name 8 in topol.top and merge.pdb does not match (H13A - H13C)
Warning: atom name 9 in topol.top and merge.pdb does not match (H13B - C14)
Warning: atom name 10 in topol.top and merge.pdb does not match (H13C - 
H14A)
Warning: atom name 11 in topol.top and merge.pdb does not match (H14A - 
H14B)
Warning: atom name 12 in topol.top and merge.pdb does not match (H14B - 
H14C)
Warning: atom name 13 in topol.top and merge.pdb does not match (H14C - C15)
(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 1308]:
   30017 non-matching atom names
   atom names from topol.top will be used
   atom names from merge.pdb will be ignored
-----------------------------------------------------------------------------------------


I am using Gromacs-4.6.5. I am just wondering why the warning 1 appears?
For Warning 2, I checked the name in my pdb file and the one from 
charmm36.ff, they are consistent with each other. I don't understand why 
the atom name doesn't match with each other.

Here is my topol.top file:


-----------------------------------------------------------------------------------------
; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"
#include "popg.itp"

[ moleculetype ]
; Name            nrexcl
POPC       3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
; residue   1 POPC rtp POPC q  0.0
      1        NTL      1   POPC      N      1       -0.6 14.007   ; 
qtot -0.6
      2       CTL2      1   POPC    C12      2       -0.1 12.011   ; 
qtot -0.7
      3       CTL5      1   POPC    C13      3      -0.35 12.011   ; 
qtot -1.05
      4       CTL5      1   POPC    C14      4      -0.35 12.011   ; 
qtot -1.4
.
.
.
; Include Position restraint file
#ifdef POSRES_POPC
#include "popc.itp"
#endif

; Include water topology
#include "charmm36.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000
#endif

; Include topology for ions
#include "charmm36.ff/ions.itp"

[ system ]
; Name
PCPG

[ molecules ]
; Compound        #mols
POPC    112
POPG    28
SOL    9595
-----------------------------------------------------------------------------------------


thank you very much.

Albert