Re: [gmx-users] Converting a solvent box file from Amber

2010-03-19 Thread Justin A. Lemkul
Justin A. Lemkul wrote: Simone Cirri wrote: Hi everyone, I'm trying to set up a MD with the AMBER99 force field of a small protein in DMSO. I found suitable parameters for DMSO and AMBER and I built my dmso.itp . The problem comes now: to solvate my protein, I also need a dmso.gro solvent b

Re: [gmx-users] Converting a solvent box file from Amber

2010-03-19 Thread Justin A. Lemkul
Simone Cirri wrote: Hi everyone, I'm trying to set up a MD with the AMBER99 force field of a small protein in DMSO. I found suitable parameters for DMSO and AMBER and I built my dmso.itp . The problem comes now: to solvate my protein, I also need a dmso.gro solvent box. I could not find a way

Re: [gmx-users] Converting a solvent box file from Amber

2010-03-19 Thread David van der Spoel
On 3/19/10 1:32 PM, Simone Cirri wrote: Hi everyone, I'm trying to set up a MD with the AMBER99 force field of a small protein in DMSO. I found suitable parameters for DMSO and AMBER and I built my dmso.itp . The problem comes now: to solvate my protein, I also need a dmso.gro solvent box. I cou

[gmx-users] Converting a solvent box file from Amber

2010-03-19 Thread Simone Cirri
Hi everyone, I'm trying to set up a MD with the AMBER99 force field of a small protein in DMSO. I found suitable parameters for DMSO and AMBER and I built my dmso.itp . The problem comes now: to solvate my protein, I also need a dmso.gro solvent box. I could not find a way to obtain it, so I searc