Re: [gmx-users] Help in parametrisation

2010-06-25 Thread Justin A. Lemkul
onetwo wrote: Hello Justin, Thanks for the reply. Sorry to say but I chose the GROMOS force field as for that topology of the ligands could be prepared by PRODRG and I followed tutorials available for Gromacs and most of them used GROMOS forcefield and for starting, parameters used in the t

Re: [gmx-users] Help in parametrisation

2010-06-25 Thread onetwo
Hello Justin, Thanks for the reply. Sorry to say but I chose the GROMOS force field as for that topology of the ligands could be prepared by PRODRG and I followed tutorials available for Gromacs and most of them used GROMOS forcefield and for starting, parameters used in the tutorials helped me

Re: [gmx-users] Help in parametrisation

2010-06-24 Thread Justin A. Lemkul
onetwo wrote: Thanks Justin for the help, I have Manganese in my protein with other two ligands at the active site. I am using GROMOS96 43a1 force field. Mangnese may have topology similar to Magnesium 2+, What I found is that Assuming a transition metal "may" be similar to another species

Re: [gmx-users] Help in parametrisation

2010-06-23 Thread onetwo
Thanks Justin for the help, I have Manganese in my protein with other two ligands at the active site. I am using GROMOS96 43a1 force field. Mangnese may have topology similar to Magnesium 2+, What I found is that I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate

Re: [gmx-users] Help in parametrisation

2010-06-23 Thread onetwo
Thanks Justin for the help, I have Manganese in my protein with other two ligands at the active site. I am using GROMOS96 43a1 force field. Mangnese may have topology similar to Magnesium 2+, What I found is that I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate

Re: [gmx-users] Help in parametrisation

2010-06-23 Thread Justin A. Lemkul
onetwo wrote: Hello All, I am new in this field, and I want to do simulation study on one of the protein conatining a metal ion and study its ability to form co-oridnation bond with other ligand, which is not defined in GROMOS force field which I have tried. If this choice of force field is

[gmx-users] Help in parametrisation

2010-06-23 Thread onetwo
Hello All, I am new in this field, and I want to do simulation study on one of the protein conatining a metal ion and study its ability to form co-oridnation bond with other ligand, which is not defined in GROMOS force field which I have tried. If this choice of force field is correct for such