[gmx-users] Changing atom names from pdb to gro in editconf

[Rebeca García Fandiño]

Dear Gromacs users,
a general question about editconf...
When I convert a pdb with 4 letters in the atom names into a gro file, the atom names change. For example, a pdb of the type:

TITLE     Great Red Owns Many ACres of Sand
REMARK    THIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  60.00  60.00  90.00 P 1           1
MODEL        1
ATOM      1 1C11 MOL     1      19.010  17.630  10.250  1.00  0.00
ATOM      2 1O20 MOL     1      20.210  18.360  10.310  1.00  0.00
ATOM      3 1C27 MOL     1      21.300  17.720  10.980  1.00  0.00
ATOM      4 1C20 MOL     1      22.230  17.130   9.920  1.00  0.00
ATOM      5 1C13 MOL     1      23.410  16.460  10.620  1.00  0.00
[...]

is converted into this .gro file after "editconf"

GroFile
 1836
    1MOL   C111    1   1.901   1.763   1.025
    1MOL   O201    2   2.021   1.836   1.031
    1MOL   C271    3   2.130   1.772   1.098
    1MOL   C201    4   2.223   1.713   0.992
    1MOL   C131    5   2.341   1.646   1.062
[...]

I am trying to obtain a .tpr file from a structure file and topology file, using General Charmm force field and I am having problems because this reordering in the names of the atoms. Even using the .pdb in the step of "grompp" the program complains about the atom names differences:

Warning: atom name 1 in topologia_complejo.top and complejo_2udades_solvatado.pdb does not match (1C11 - C111)
Warning: atom name 2 in topologia_complejo.top and complejo_2udades_solvatado.pdb does not match (1O20 - O201)
Warning: atom name 3 in topologia_complejo.top and complejo_2udades_solvatado.pdb does not match (1C27 - C271)
Warning: atom name 4 in topologia_complejo.top and complejo_2udades_solvatado.pdb does not match (1C20 - C201)
Warning: atom name 5 in topologia_complejo.top and complejo_2udades_solvatado.pdb does not match (1C13 - C131)

I have tried GROMACS 5.0 and GROMACS 4.6, and in both cases I have found the same problem.

Any suggestion will be much appreciated!!!

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain