[gmx-users] g_sas problem?

[Justin Lemkul]

On 1/5/15 4:01 PM, Albert wrote:
> Hello:
>
> 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?
>

Well, clue #1:

WARNING: could not find a Van der Waals radius for 122 atoms

You've got something in the system that isn't covered by vdwradii.dat; find out 
what that is and you'll start to diagnose the issue.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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