[gmx-users] Topology for Charmm, regarding

2017-12-15 Thread RAHUL SURESH
Dear all I have generated a structure.par file using ffTK toolkit of VMD. To use it in gromacs I have generated the structure.top file using topoltool plugin of vmd. 1. Now, how can i generate "itp" file to carry out, protein-ligand simulation? 2. Will it be sufficient if I generate "gro" file

Re: [gmx-users] Topology for charmm

2017-03-21 Thread Justin Lemkul
On 3/21/17 4:54 AM, RAHUL SURESH wrote: how to generate charmm topology file for gromacs using charmm2gmx python script? I have generated the stream file using cgenff.parachem server.? I wish to have a comprehensive answer Use the CGenFF conversion script here:

[gmx-users] Topology for charmm

2017-03-21 Thread RAHUL SURESH
how to generate charmm topology file for gromacs using charmm2gmx python script? I have generated the stream file using cgenff.parachem server.? I wish to have a comprehensive answer -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] topology for charmm

2017-03-20 Thread Justin Lemkul
On 3/20/17 7:13 AM, RAHUL SURESH wrote: How to reduce param and charge penality while generating stream file? Large penalties indicate poor similarity with existing groups in the force field. In those cases, you have to manually reparametrize those groups using the published CGenFF

[gmx-users] topology for charmm

2017-03-20 Thread RAHUL SURESH
How to reduce param and charge penality while generating stream file? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!