[gmx-users] SASA calculation

Justin Lemkul jalemkul at vt.edu
Thu Apr 18 16:45:23 CEST 2019

On 4/18/19 10:38 AM, Pandya, Akash wrote:
> Hi all,
> I'm trying to calculate the SASA of my protein, however I am getting this warning message:
> 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.
> How can I fix this?

Pass a .tpr file to -s instead of a coordinate file. Unless there's 
anything unusual in the system, it may not matter. The only weird stuff 
is when you have something like mercury (Hg) which is guessed as a 
hydrogen, or calcium (Ca), which is guessed as a carbon.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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