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

[Justin Lemkul]

On 2/7/15 5:29 PM, Rebeca García Fandiño wrote:
> 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!!!
>

This is an unintended consequence of trying to rename things that may not 
conform to other standards.  Please file a report on redmine.gromacs.org; it's 
not necessarily a bug, per se (note the comments in src/gromacs/fileio/pdbio.c 
in the write_pdbfile_indexed() function), but it does cause problems, so a more 
general solution is probably needed.

In the meantime, in this case it is safe to use -maxwarn to override the 
problem, since there is no actual error or mismatch.  Or just don't convert to 
PDB before running grompp (there's no need to, and you don't gain anything).

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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