Re: [gmx-users] pds files without bond information

2013-02-21 Thread Erik Marklund
On Feb 20, 2013, at 9:58 PM, Erik Marklund wrote: Hi, pdb2gmx generate the connectivity from the residue and atom sequences (the file format specs state the order in which they appear) and the distances between atoms. This is fairly robust as long as the coordinates aren't unusually bad.

Re: [gmx-users] pds files without bond information

2013-02-20 Thread Justin Lemkul
On 2/20/13 1:59 PM, cdo wrote: Hi all, I'm new to Gromacs with a very basic question while I was reading tutorials. Tried to search this but I couldn't narrow down to useful discussions so far. It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But this particular pdb file

Re: [gmx-users] pds files without bond information

2013-02-20 Thread Erik Marklund
Hi, pdb2gmx generate the connectivity from the residue and atom sequences (the file format specs state the order in which they appear) and the distances between atoms. This is fairly robust as long as the coordinates aren't unusually bad. For instance, if two carbons are located at ~1 C-C

[gmx-users] pds files without bond information

2013-02-20 Thread cdo
Hi all, I'm new to Gromacs with a very basic question while I was reading tutorials. Tried to search this but I couldn't narrow down to useful discussions so far. It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But this particular pdb file do not have all the connectivity i