Hello everyone,
I tried to generate the topology and .gro file for a protein in GROMACS using pdb2gmx command. When I visualise the .gro file in VMD (new cartoon representation) some of the helices are missing (but residues are there) which are seen in case of the .pdb file. The choice of all atom/united atom force fields are giving same result.
This anomaly(?) is for a particular pdb file (generated directly from x-ray data, not yet published).
What may have caused this change? Is there something more that should be taken care of?
Write your opinions in the comments. Thank you.
I didn't face such a problem so far, but VMD uses STRIDE to predict and render secondary structure by default. Perhaps your PDB file contains additional information on s. structure?
Moreover, have you tried to load your pdb file first and than load a *.gro file as an additional data?
PDB coordinates have one additional decimal place relative to .gro formatted coordinate files. Probably there's enough deviation from ideality in some helices that VMD incorrectly assigns the secondary structure.
@Rafal
I directly load the .gro file. pdb2gmx only changes the .pdb files by adding hydrogens to the appropriate place. So according to me the secondary structures should remain intact. That's why I am concerned.
How can I load the pdb first and then the gro as additional data?
I can get the ribbon structure of my peptide by NewRibbon representation. But NewCartoon doesn't work and again shows the ribbons instead of the beta sheets. All of the renames and IDs are correct. Does anyone know what the problem is?
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