GROMACS version:2022
GROMACS modification: Yes/No
I am trying to find SASA for a protein surface, which I provide in the index file. My system is coarse-grained using the MARTINI force field. I am getting a warning, and I am providing it below. Please suggest to me where things are going wrong.
gmx sasa -f pbc.xtc -s …/npt.tpr -o sasa_SLT_m2.xvg -n INP-loop-BB-SC.ndx -pbc yes -xvg none -tu ns -odg FES_SLT_m2.xvg
Reading file …/npt.tpr, VERSION 2022 (single precision)
Reading file …/npt.tpr, VERSION 2022 (single precision)
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
Michael Scharf
The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
of Surface Area and Volume and to Dot Surface Contouring of Molecular
Assemblies
J. Comp. Chem. 16 (1995) pp. 273-284
-------- -------- — Thank You — -------- --------
Free energy of solvation predictions:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- — Thank You — -------- --------
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. Note, that this functionality may
be removed in a future GROMACS version. Please, consider
using another file format for your input.
NOTE: From version 5.0 gmx sasa uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- — Thank You — -------- --------
WARNING: could not find a Van der Waals radius for 42 atoms
Reading frame 0 time 0.000
Back Off! I just backed up sasa_SLT_m2.xvg to ./#sasa_SLT_m2.xvg.1#
Last frame 2000 time 1000.000
Analyzed 2001 frames, last time 1000000.000
There is no information about Martini bead radii in GROMACS, so it’s not possible to calculate the SASA with the default settings. However, you can provide these radii yourself. From your GROMACS installation location, copy the share/gromacs/top/vdwradii.dat to the directory where you are running gmx sasa. Now you need to edit the file in a text editor and set the values corresponding to Martini beads. See information in Parametrization of a new small molecule – Martini Force Field Initiative (especially Parametrization of a new small molecule – Martini Force Field Initiative) and https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f3ed2d35156b45b4e2624f/original/supporting-information-for-martini-3-coarse-grained-force-field-small-molecules.pdf how to set the correct radii values.
@MagnusL Thank you so much for the information. I have fetched the file from the location and have manually edited the radii values for the corresponding beads. But how does the gmx sasa command read the file from my working directory? Please let me know. Thanks once again for your tme and advice.
Files (with file names matching the data file that should be loaded) in the local directory has the highest priority, followed by the GROMACS share/top directory indicated by the GMXLIB environment variable.
vdwradii_CG.dat (9.6 KB)
I have modified the vdwradii.dat as per the specification given in the MARTINI website and have tried placing the modified file in the current directory and in the gmx executable path also. I am attaching the modified file for your reference. But I get the same error as before:
Command: gmx sasa -f pbc.xtc -s …/npt.tpr -o sasa_TQT_m1.xvg -n INP-loop-BB-SC.ndx -pbc yes -xvg none -tu ns -odg FES_TQT_m1.xvg -ndots 240 -probe 0.191
WARNING: could not find a Van der Waals radius for 45 atoms
Reading frame 0 time 0.000
Back Off! I just backed up sasa_TQT_m1.xvg to ./#sasa_TQT_m1.xvg.1#
Back Off! I just backed up FES_TQT_m1.xvg to ./#FES_TQT_m1.xvg.1#
Last frame 2000 time 1000.000
Analyzed 2001 frames, last time 1000000.000
The file must be called vdwradii.dat otherwise it certainly won’t be found.
Thank you so much for helping me out.
Hi, I have the same problem here. I’m also using CG models and calculating the surface area with gmx sasa. The vdwradii.dat file is in the execution folder and with the same name.
I ran this command: gmx sasa -f last_2us.xtc -s step7_production.tpr -ndots 4800 -probe 0.235 -o out_sasa.xvg -n …/…/input/index.ndx
and I got this error:
…
WARNING: Error in file vdwradii.dat at line 1551 ignored
WARNING: Error in file vdwradii.dat at line 1552 ignored
WARNING: Error in file vdwradii.dat at line 1553 ignored
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. Note, that this functionality may
be removed in a future GROMACS version. Please, consider
using another file format for your input.
NOTE: From version 5.0 gmx sasa uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- — Thank You — -------- --------
WARNING: could not find a Van der Waals radius for 619 atoms.
I checked the document but still don’t know what should be the correct atom names ( either BB/SC1 in my gro file or SC1/SC2… in the .itp file) I tried both but non of them worked. Also I don’t know what should be under the ’ ; Masses for vsite construction’ section. Here’s the vdwradii database file I used as input.
vdwradii.dat (11.5 KB)