Re: R: Re: [gmx-users] numbering of .gro file

2011-05-16 Thread Justin A. Lemkul
Anna Marabotti wrote: 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 presen

R: Re: [gmx-users] numbering of .gro file

2011-05-16 Thread Anna Marabotti
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

Re: R: Re: [gmx-users] numbering of .gro file

2011-05-13 Thread Justin A. Lemkul
Anna Marabotti wrote: Dear Justin, thank you very much for infos. I was aware that in Gromacs 4.5.4 pdb2gmx does not renumber the PDF file anymore; what seems strange to me is that Gromacs 4.5.4 "backnumbered" also a .gro file that was already renumbered by 4.0.7, without using pdb2gmx (I only

R: Re: [gmx-users] numbering of .gro file

2011-05-13 Thread Anna Marabotti
Dear Justin, thank you very much for infos. I was aware that in Gromacs 4.5.4 pdb2gmx does not renumber the PDF file anymore; what seems strange to me is that Gromacs 4.5.4 "backnumbered" also a .gro file that was already renumbered by 4.0.7, without using pdb2gmx (I only took the nvt.gro and nvt.t