Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-09 Thread Nikolaos Michelarakis
Hello again, This what I have been trying to do so far. This is the command to run the script: ./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff and this is the error I have been getting along with 2 Notes: NOTE2: Please be sure to use the same version of CGenFF in your

Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-02 Thread Nikolaos Michelarakis
Dear Justin, Thank you very much for your reply. I have tried the converter but I think I don't have enough experience to get the CHARMM files working properly with the converter. If I sent you the files, would it be possible to do it for me or guide me through it? Thanks again, Nicholas On

Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-02 Thread Justin Lemkul
On 7/2/14, 10:55 AM, Nikolaos Michelarakis wrote: Dear Justin, Thank you very much for your reply. I have tried the converter but I think I don't have enough experience to get the CHARMM files working properly with the converter. If I sent you the files, would it be possible to do it for me