[gmx-users] SASA calculation
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.
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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