Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

On 5/20/17 8:28 AM, Dawid das wrote: Hi Mark, Thank you. Actually I want to do some QM/MM calculations with CHARMM22 for MM part but not using GROMACS and not all things that are implemented in GROMACS are available in my QM/MM package. Nevertheless, I still want to gather as much data as poss

Re: [gmx-users] pdb2gmx do not work for unstable conformations

Hi, Some of your PDB files are malformed, which you could see with the less tool, or probably anything else. The first line, containing N, leads with strange characters, which stops pdb2gmx recognizing that they start with "ATOM," since they don't. Then N are recognized as missing. Mark On Sat,

[gmx-users] pdb2gmx do not work for unstable conformations

Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, predicted by Rosetta with different ddG. After running pdb2gmx, I found that the structures with lower ddG (more stable) all perform okay; while structures with higher ddG (less stable) got fatal error: Fatal error: Residu

Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

Hi Mark, Thank you. Actually I want to do some QM/MM calculations with CHARMM22 for MM part but not using GROMACS and not all things that are implemented in GROMACS are available in my QM/MM package. Nevertheless, I still want to gather as much data as possible. Best wishes, Dawid 2017-05-19 22: