Questions about visualization with VMD about gromacs-fda HOT 10 CLOSED

I am waiting for a response of the developer of the VMD plugins. To my present knowledge the VMD plugins are deprecated and were replaced by the gmx analysis modules.

from gromacs-fda.

I will reactivate the VMD plugins, because of the more flexible usage. Although the gmx analysis module 'fda_graph' is easier to use, it is very limited to handle more complex force networks by using the pdb format.

from gromacs-fda.

I will reactivate the VMD plugins, because of the more flexible usage. Although the gmx analysis module 'fda_graph' is easier to use, it is very limited to handle more complex force networks by using the pdb format.

Thanks a lot. I've also tried fda_graph to generate a PDB file. But it seems the PDB file don't have the sequence information, and only generate a network structure. May I know how should I overlap that to my original protein structure?

from gromacs-fda.

Yes, the pdb file produced by fda_graph contains only the network information. With VMD you can load the structure or the trajectory as second input. Using the flag '-pymol' a pml file will generated which can be loaded with Pymol.

from gromacs-fda.

Yes, the pdb file produced by fda_graph contains only the network information. With VMD you can load the structure or the trajectory as second input. Using the flag '-pymol' a pml file will generated which can be loaded with Pymol.

When I load the structure or trajectory into the pdb with VMD, always get errors:
ERROR> Mismatch between existing molecule or structure file atom count and coordinate or trajectory file atom count.
It seems the number of atoms in the pdb file from fda_graph is neither the number of protein atoms nor system atoms from the original structure.
My .pfi file:

onepair = summed
group1 = Protein
group2 = Protein
atombased = no
residuebased = pairwise_forces_scalar
type = all
time_averages_period = 0

and running fda_graph as:

gmx_fda fda_graph -i example.pfr -s example.gro -f example.trr -n example.ndx -o example.pdb

selecting group 3 (C-alpha) for residue model points (the only one can match).

from gromacs-fda.

You have to load it as two separate molecules:

1. The example.gro file for the atomic structure. The gro-file contains the reoriented coordinates.
2. Load example.pdb as new molecule (not into the first structure)

If you are using '-frame skip ' you have to generate a suitable trajectory, which has the same frames.

from gromacs-fda.

Sorry, what I mean is actually something like Fig. 2B in doi: 10.1186/1471-2105-12-101. So the Fig. 2B is actually by VMD plugins?
And since the deprecated VMD plugins, can I take the summation of the absolute values of scalar_force column in .pfa file for each atom as the force on atom? (or in .pfr file for each residue, is this the same as the equation(3) in the paper?)

from gromacs-fda.

The publication you mentioned was before I was working on FDA, but I would also say that it was produced with the VMD plugins. The fda_graph is only for the network graphs. Therefore, I would like to ask you for some patience. I will provide the VMD plugins in the next days.

from gromacs-fda.

Thanks a lot!

from gromacs-fda.

Please find the VMD plugins in the new repository https://github.com/HITS-MBM/gromacs-fda-vmd

from gromacs-fda.