[gmx-users] errors with charmm36 ?

[Justin Lemkul]

On 1/14/14, 6:41 AM, Albert wrote:
> 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
>

This error suggests you have a malformatted .mdp file, so make sure you have no 
hidden characters and are always using a plain-text editor.

> 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.
>

The topology lists atoms in a different order than the input coordinate file. 
 From the topology you show below, atom 3 should be C13, but in the coordinate 
file, atom 3 is H12A.

-Justin

> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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