[gmx-users] atom indexing in top and gro files

[Ling Chan]

Dear Colleague,

I just wonder how exactly are the atom numbering in gro files and in the “atoms” section of topology files used. There does not seem to be much information on the file format manual pages. (i.e. http://manual.gromacs.org/documentation/current/reference-manual/file-formats.html#gro and http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2). In the given examples, they are simply 1,2,3,4,… But if that has to be the case, why have this field to begin with? So I suppose there has to be certain rules, perhaps to map atoms from the topology file to the gro file.

According to this archived post, https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg17227.html, only the ordering of the lines is important. Does it mean that if in the topology file I have in the “molecules” field
  Protein_chain_A    1
  Protein_chain_B    1
 SOL            831
and in the gro file they are ordered as ChainA, then water, then ChainB, then things will break? Alternatively, if within some residues the atom ordering differs between the topology file the the gro file, (e.g. CD NE OE as opposed to CD OE NE), then things will break even if I “reorder” them by atom indices?

And if the atom indices are really ignored, can I just put 999 on all lines?

I understand that if I use pdb2gmx it will take care of things, but I need to write my own utilities to produce gro and top files.

Thank you in advance!

Ling

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