Dear gmx-users, first let me resume my attempts on this question. 1) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top I obtained a .gro file in which the numbering of each chain correctly starts from 21 to 379 in both chains, but no chain ID is present, so I cannot distinguish residues of chain A from residues of chain B
2) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -renum I obtained a .gro file in which the numbering of each chain starts from 1 to 359 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B 3) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -chainsep id I obtained a .gro file in which the numbering of each chain starts from 21 to 379 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B. 4) Using: pdb2gmx -f my_protein.pdb -o my_protein.pdb -p my_protein.top I obtained an output .pdb file in which the numbering and the chain ID of the input .pdb file are kept (and so I can distinguish between the residues of chain A and of chain B. However, when I continue with editconf+genbox and add 22586 water molecules, I have the problem of more than 9999 residues, which is not compatible with a .pdb format, so the numbering of the residues restarts twice from zero. My question is: can I distinguish chain A and B of my protein (either with a chain ID or with a consecutive numbering of the two chains) AND have a file format compatible with more than 9999 residues using Gromacs only? Thank you very much Anna Date: Fri, 13 May 2011 09:54:38 -0400 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] numbering of .gro file To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Mark, > thank you also for your suggestion, indeed using the nvt.gro file with the > sequential numbering I was able to distinguish the contributions from both > chains, instead of seeing them superimposed. > Now I have another question. I used pdb2gmx to prepare another file for > simulation (it is the same protein as above, with a mutation). The pdb file > contains two identical chains numbered starting from 21 to 379, marked with > chain ID A and B. > Using the command line: > pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top > I obtained a .gro file in which the numbering correctly starts from 21 to > 379 in both chains, but no chain ID is present. I also tried to use > -chainsep, but nothing changed. So my (last) question is: is there any way > to avoid renumbering the file, but without obtaining a superposition of > residue numbers in both subunits? In other workds: is there a possibility to > leave some form of "chain identifier" in the .gro file? Or the only way to > obtain unambiguous identification of each residue is to renumber the file? There are no chain identifiers in .gro format. If you want them, use .pdb instead. You can make use of a variety of formats for just about all the Gromacs tools; there is no requirement for .gro. If your input .pdb file has chain identifiers, so too should the output structure. -Justin -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
