Re: [gmx-users] The charge of cofactor and ligand

2013-09-24 Thread Justin Lemkul
On 9/24/13 7:16 AM, aixintiankong wrote: Dear prof. The format of parameters is convenient to the software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to the itp format for gromacs. so i use acpype to get itp format. i just doubt th

Re: [gmx-users] The charge of cofactor and ligand

2013-09-23 Thread Justin Lemkul
On 9/23/13 5:10 PM, aixintiankong wrote: Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negati

Re: [gmx-users] The charge of cofactor and ligand

2013-09-23 Thread Mark Abraham
How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong wrote: > Dear prof, > can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand > and then use acpype to generate GAFF force field parameter for the NAD+ and > ligand? > -- > gmx-users mailin

[gmx-users] The charge of cofactor and ligand

2013-09-23 Thread aixintiankong
Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search th