Re: [gmx-users] creating topology for ligand

ok thanks. On 2 Mar 2018 22:25, "Justin Lemkul" wrote: > > > On 3/2/18 12:18 PM, neelam wafa wrote: > >> Thanks Justin >> >> Can you please suggest me any article or reading that can help me to >> understand the factors to be considered while choosing a force field or to >>

Re: [gmx-users] creating topology for ligand

On 3/2/18 12:18 PM, neelam wafa wrote: Thanks Justin Can you please suggest me any article or reading that can help me to understand the factors to be considered while choosing a force field or to parameterize the ligand? I could suggest hundreds. Start with even a basic Google search for

Re: [gmx-users] creating topology for ligand

Thanks Justin Can you please suggest me any article or reading that can help me to understand the factors to be considered while choosing a force field or to parameterize the ligand? On 1 Mar 2018 18:14, "Justin Lemkul" wrote: > > > On 3/1/18 8:03 AM, neelam wafa wrote: > >>

Re: [gmx-users] creating topology for ligand

On 3/1/18 8:03 AM, neelam wafa wrote: Dear gmx users I am trying to run a protein ligand simmulation. How can i create topolgy for ligand. prodrg topology is not reliable then which server or software can be used? can topology be created by T LEEP off ambertools package for gromacs?? The

[gmx-users] creating topology for ligand

Dear gmx users I am trying to run a protein ligand simmulation. How can i create topolgy for ligand. prodrg topology is not reliable then which server or software can be used? can topology be created by T LEEP off ambertools package for gromacs?? secondly how to select the boxtype as I am new to