[gmx-users] g_sas

[Justin Lemkul]

On 8/16/14, 9:09 PM, Eric Smoll wrote:
> Hello Rajat and Justin,
>
> I am deeply grateful for the responses. Thank you.
>
> Rajat,
>
> You said: "By vacuum accessible surface area, I assume that you mean the
> area defined
> the surface of the interstitial volume."
>
> I am looking for the vacuum accessible surface area at a vacuum-liquid
> interface. I am very sorry for the confusion. Instead of carrying on with a
> conversation on the nature of the g_sas simulation output, perhaps I should
> just try to get a surface calculation working and examine it myself.
>
> Rajat and Justin,
>
> The file "vdwradii.dat" only appears in a few places in the manual and it
> is unclear if g_sas actually uses it. I made a local copy of
> share/gromacs/top, edited vdwradii.dat with the following format
> {3-LETTER-RESIDUE-NAME     .TOP/.GRO-FILE-ATOM-NAME     RADIUS-IN-NM} and
> updated the GMXLIB environment variable to point to this edited directory
> with "export path/to/new/top". I created a .tpr file with grompp and made a
> call with g_sas as I described before. I get the same error:
>

There is no need to go to such lengths; just make a copy of vdwradii.dat in your 
working directory and edit it as needed.  Gromacs tools, by default, search for 
library files in the working directory first, then $GMXLIB.

> 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 640 atoms
> 29440 out of 34560 atoms were classified as hydrophobic
>
> As I mentioned before, 640 matches the number of molecules I have in the
> simulation. I have no idea why the g_sas is not referencing the sigma
> values in my ffnonbonded file or my vdwradii.dat. I have used vim regular
> expression capabilities to ensure that every atom in my .gro/.top files is
> represented in the vdwradii.dat file. More guidance would be much
> appreciated.
>

The output indicates you have 1 atom per molecule that is somehow problematic. 
What molecules are you dealing with?  Any bizarre atoms?  What changes did you 
make in vdwradii.dat?  Does adding -debug 1 to the command line print anything 
useful in diagnosing?

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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