Re: [gmx-users] Strange behavior from g_sas

On 30/03/2011 9:21 PM, Terry wrote: Hi Mark, The output is like this: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. 2565 out of 4931 atoms were

Re: [gmx-users] Strange behavior from g_sas

Hi Mark, The output is like this: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. 2565 out of 4931 atoms were classified as hydrophobic Back Off! I

Re: [gmx-users] Strange behavior from g_sas

On 30/03/2011 5:58 PM, Terry wrote: Hi, all, I have four trajectories which I want to analyze Surface on. So I run for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done But the strange thing is, g_sas analyzed the first

[gmx-users] Strange behavior from g_sas

Hi, all, I have four trajectories which I want to analyze Surface on. So I run for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done But the strange thing is, g_sas analyzed the first three trajectories, but gave a "seg