[gmx-users] Changing atom names from pdb to gro in editconf
jalemkul at vt.edu
Sat Feb 7 23:40:27 CET 2015
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"
> 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 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
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