How to convert representation into a PDB file?

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1

GROMACS version:
GROMACS modification: Yes/No
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Hi,

Does anybody have advice on how to convert my VMD state/visualisation state into a PDB file?

2

Though, It is not the scope of this forum, but I will try to answer.

In TK console: Try followings

set sel [atomselect top "all"] 
$sel writepdb "out.pdb"
3

Hi,

Thank you for the reply. I loaded my visualisation state and then wrote commands for the TK console but I obtain the original PDB file?

I have changed the structure using graphical representations but nothing has changed.

4

PDB file does not save graphical representations. It is mostly coordinate file (though it does include some other things too) so what you are essentially are doing is saving the x,y,z coordinates, residue names, residue numbers, atom numbers and atom names.

5

I have acquired my PDB file from CHARMM-GUI. I would like to rotate this at 90 degrees and keep this orientation fixed. Do you have any advice on how this could be done?

6

The orientation of the system is arbitrary. Why do you need to rotate the system? In any case, gmx editconf -rotate, would be the way to do it.

7

I am carrying out a similar simulation in relation to particular paper but they have two different orientations of the same protein that rotate at 90 degrees and carried out a simulation on a bare silica surface. However, the paper has not specified the rotation around the axis. A link to the image of the structure is provided here:

Also, can I carry out the orientation on Tk console or only on Gromacs?

Thank you for your response.

8

OK, relative orientation of molecules is important and you can carry out rotating the protein either with editconf or whatever other tools you want. This has nothing to do with visual representation, however, which is what your earlier question was. You can probably do the rotation in VMD and export the manipulated coordinates, but certainly editconf will do this.

9

I am reiterating what already mentioned in previous answers, changing view by mouse/keyboard also changes frame of reference. So no transformation takes place. You need to use explicit transformation using VMD commands (e.g.: move, moveby). Probably, you may try something like that.

set sel [atomselect top "all"] 
set rotmat [transaxis z 90]  # adjust axis (x/y/z) and angle
$sel move $rotmat  
$sel writepdb "out.pdb"
10

I have found it easier to orientate the protein the way I want using the mouse. How do I save this new orientation as a PDB file?

11

In VMD - File -> Save Coordinates

12

How to retrieve pdb file from VMD after simulation? I simulating for 20ns using GROMACS and want to retrieve the pdb at 20 ns?

13

gmx trjconv can be used to extract specific frames, as is done in this tutorial

14

Hi,
I have built the system first by aligned the peptide in the desired direction and set up the simulation. Here