RE: [gmx-users] Energy minimisation of solvated protein - Tutorial

GROMACS users Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gr

Re: [gmx-users] Energy minimisation of solvated protein - Tutorial

Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher wrote: > Hi, > > I have the same

Re: [gmx-users] Energy minimisation of solvated protein - Tutorial

Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output