[gmx-users] g_sas problem?

Albert mailmd2011 at gmail.com
Mon Jan 5 22:02:05 CET 2015


I am interested in the solvent access surface area change after ligand 
binding to protein. I performed protein/ligand complex MD in Gromacs. I 
try to obtain SASA with command:

g_sas_mpi -f nvt.xtc -nopbc -s nvt-4.tpr -o area.xvg -n

Reading frame       0 time    0.000   Select a group for calculation of 
surface and a group for output:
Select a group: 26
Selected 26: 'Protein_UNK'
Select a group: 26
Selected 26: 'Protein_UNK'

The job finished with warnings:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
          based on residue and atom names, since they could not be
          definitively assigned from the information in your input
          files. These guessed numbers might deviate from the mass
          and radius of the atom type. Please check the output
          files if necessary.

WARNING: could not find a Van der Waals radius for 122 atoms
2818 out of 4779 atoms were classified as hydrophobic

And I obtained two files:
area.xvg   atomarea.xvg

for area.xvg file I obtained following:

@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
          0     72.9665     106.739     179.705     876.487
          2     75.0095     108.485     183.494     906.284
          4     73.8583     108.529     182.387     879.551
          6     73.1028     106.306     179.409      871.09
          8     72.8699     105.537     178.406     863.294
         10     72.8653     105.615      178.48      872.05

but values in atomarea.xvg are all "0 0"

I am just wondering what's the problem?

Thank you very much.


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