[gmx-users] errors with charmm36 ?

[hubert santuz]

Hi,

I just came across this issue a few days ago (with charmm-gui also).
In fact, atoms C13, C14 and C15 should be just after the C12 atoms in 
the pdb (to match the itp file).

Here a piece of code that I used to retrieve the good order for all POPC 
molecules in your gro file (on unix platform) :

for i in `grep "POPC   C13" yourfile.gro --line-number | awk -F: '{print 
$1}'`
do
     j=$((i-3))
     (echo "${i}m${j}"; echo w; echo q ) | ed yourfile.gro
done

Basically, ed is used to move each line "POPC C13", 3 lines above. (6 
lines for C14 and 9 lines for C15).

Beware also that a  certain number of atom's name are wrong also :
"0C21" (charmm-gui file) --> 'C210' (itp file)
"1H10" --> 'H101'
etc.
In this case, 'sed' is a great tool ;)

Cheers,
Hubert


Le 14/01/2014 14:22, Justin Lemkul a écrit :
>
>
> 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
>