[gmx-users] Problem with editconf

[abhishek khetan]

Hello everyone,

I am a new user and am trying to generate a solventbox for non-water
solvation. the solvent in this case is dimethoxyethane(DME), the *.pdb for
which i generated using the software openbabel, because i had only its xyz
format at hand. Now using this generated pdb i am giving the command on my
cluster which has gromacs/5.0.4 installled
$ gmx_mpi editconf -f DME_new.pdb -bt o -d 0.5 -density 868.3

for which the error file says:
--------------------
WARNING: all CONECT records are ignored
Volume  of input 0 (nm^3)
Mass    of input 90.1206 (a.m.u.)
Density of input inf (g/l)
--------------------


And the output is:
--------------------
Read 16 atoms
No velocities found
    system size :  0.454  0.618  0.178 (nm)
    diameter    :  0.756               (nm)
    center      :  0.000  0.000  0.000 (nm)
    box vectors :  0.000  0.000  0.000 (nm)
    box angles  :   0.00   0.00   0.00 (degrees)
    box volume  :   0.00               (nm^3)

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.
--------------------

Clearly, something is wrong with the input DME_new.pdb file because the
CONECT are all ignored. I have attached the contents of the pdb file in the
text file.

Iwant to do simulations for quite a few solvents and solutes for which the
pdb files may not be readily available. Could you please suggest a
consistent way of doing this/getting around this error ?

Best,
askhetan
-------------- next part --------------
COMPND    0066dim H10C4O2 1,2-dimethoxyethane m062x_mg3s_geom 
AUTHOR    GENERATED BY OPEN BABEL 2.3.2
HETATM    1  C   LIG     1      -0.062   0.753   0.000  1.00  0.00           C  
HETATM    2  C   LIG     1       0.062  -0.753   0.000  1.00  0.00           C  
HETATM    3  O   LIG     1       1.235   1.291   0.000  1.00  0.00           O  
HETATM    4  O   LIG     1      -1.235  -1.291   0.000  1.00  0.00           O  
HETATM    5  C   LIG     1       1.235   2.694   0.000  1.00  0.00           C  
HETATM    6  C   LIG     1      -1.235  -2.694   0.000  1.00  0.00           C  
HETATM    7  H   LIG     1       2.270   3.024   0.000  1.00  0.00           H  
HETATM    8  H   LIG     1      -2.270  -3.024   0.000  1.00  0.00           H  
HETATM    9  H   LIG     1       0.732   3.089   0.889  1.00  0.00           H  
HETATM   10  H   LIG     1      -0.732  -3.089   0.889  1.00  0.00           H  
HETATM   11  H   LIG     1       0.732   3.089  -0.889  1.00  0.00           H  
HETATM   12  H   LIG     1      -0.732  -3.089  -0.889  1.00  0.00           H  
HETATM   13  H   LIG     1      -0.620   1.078   0.887  1.00  0.00           H  
HETATM   14  H   LIG     1       0.620  -1.078   0.887  1.00  0.00           H  
HETATM   15  H   LIG     1      -0.620   1.078  -0.887  1.00  0.00           H  
HETATM   16  H   LIG     1       0.620  -1.078  -0.887  1.00  0.00           H  
CONECT    1   15    2    3   13                                       
CONECT    1                                                           
CONECT    2   16    1    4   14                                       
CONECT    2                                                           
CONECT    3    1    5                                                 
CONECT    4    2    6                                                 
CONECT    5   11    3    7    9                                       
CONECT    5                                                           
CONECT    6   12    4    8   10                                       
CONECT    6                                                           
CONECT    7    5                                                      
CONECT    8    6                                                      
CONECT    9    5                                                      
CONECT   10    6                                                      
CONECT   11    5                                                      
CONECT   12    6                                                      
CONECT   13    1                                                      
CONECT   14    2                                                      
CONECT   15    1                                                      
CONECT   16    2                                                      
MASTER        0    0    0    0    0    0    0    0   16    0   16    0
END