[gmx-users] g_sas and g_hbond

[Berk Hess]

>From: Marc Vogt <mvogt at es.chem.umass.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] g_sas and g_hbond
>Date: Sun, 17 Oct 2004 14:43:43 -0400 (EDT)
>
>Using both gromacs 3.2.1 and 3.1.4 I have tried to generate a
>plot of the solvent accessible surface area for a sidechain of
>a single residue.  The plots indicate the sas for a Trp sidehain
>is 2.5 nm^2 +/- 0.3 nm^2 constantly over the entire trajectory.
>The result applies for all Trp sidechains observed.
>
>However:
>The protein clearly unfolds over the trajectory by visual inspection.
>Web based methods for SAS calculation of selected snapshot structures
>show variation.  So the real value of the sidechain SAS should not
>be constant.
>
>I also see the same behavior for g_hbond on the whole protein,
>where I choose Protein-Protein
>hbonds from the index and I see little change (other than fluctuation
>about an average), despite the fact that visual inspection shows and
>do_dssp indicates that significant hydrogen bonding is lost.
>
>I searched the archives and found one similar problem that didn't
>have a resolution.  That person was using two chains I believe.
>My system is a single chain in solvent.  It seems that with such
>drastic conformational change one would see more
>variation in such calculations.
>
>To be more specific as to the methods I used, here are my steps.
>1)  make_ndx -f protein.gro -o trps.ndx
>
>     I chose "8 & r7" to get the sidechain for residue 7.  Then quit
>
>2)  g_sas -f whole.trr -s test.tpr -n trps.ndx -o area7.xvg
>
>     I chose the field created from the above command for "8 & r7"
>
>
>The same problem occurs using an xtc file instead of trr, for multiple 
>residues,
>for different versions of GROMACS (3.2.1 and 3.1.4) on different 
>trajectories.

The problem is that you can not just select one residue.
The program will consider this residue as a single entity in a solvent.
What you want is to calculate the solvent accesible surface of the protein
and then only plot the values for one residue.
The -or option does this, but only plots averages over time.

It would be very useful if this option would be implemented.

Berk.

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