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 classified as hydrophobic
Back Off! I just backed up sas/4.area.xvg to sas/#4.area.xvg.1#
Back Off! I just backed up sas/4.volume.xvg to sas/#4.volume.xvg.1#
There were 372 inconsistent shifts. Check your topology
There were 372 inconsistent shifts. Check your topology
Segmentation fault
I have a periodic molecule, so there are many "inconsistent shifts"
lines which I ignored before.
I still don't understand why g_sas can work with the first three trjs
but the last one in the same for loop.
It sounds like g_sas doesn't cope well with periodic molecules. You
could try the trjconv pbc options, but they need not help you.
Mark
Terry
On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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 three
trajectories, but gave a "segmentation fault for the last one.
The only difference for these trjs is the number of water
molecules, hence the box size(I used NPT.) . Then I doubt
maybe the atom name I used can't be put in pdb file (some of
them are 5 letters long, and I used gro file since the very
beginning ). I deleted the -q flag and run g_sas again, seg
fault again.
After searching, I did this:
source /usr/local/gromacs/bin/GMXRC
Then g_sas worked fine( without the -q flag).
But I've already sourced GMXRC.bash.
You've either got some other installation of GROMACS that you were
using, or you changed your input files, or something about the
machine changed. Unfortunately "segmentation fault" is just a
generic error. Some idea what the output said before that might
clue people in as to why that happened.
Mark
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