Hi,
I have a difficulty in preparing my ssDNA structure for Gromacs MD. First, I had used RNAcomposer to generate the 3D structure of my ssDNA. I had edited the structure from RNA to DNA by adding methyl group in U base to T and substitute OH in ribose to H. When I dock the ssDNA on my protein using Vina, it had worked well. However, then I tried to create my topology file for Gromacs, errors message appears saying some of my atoms are not connected. How do I view and edit this in PDB? Here I attach my ssDNA. I am new to Gromacs, therefore any advice would be highly beneficial.
Additionally, there are some fragmented regions (red) in the protein . . .
Hi Sabri,
As Uttam mentioned, you can edit those ribose. In addition a short energy minimisation using swisspbdviewer may also help you. Even then if ur topology is not built, try using prodrg to generate gromacs topology for ur ssDNA
CHEERS
Thank you all, I found your suggestions are very helpful! The structures were after-docking structures where I choose the pose with the lowest binding energy and save the .PDBQT file to .PDB. file. Although Pymol can visualize the docking conformation and analyze the H-bonds formed in the docking, I notice that the .text file it had becomes hard to edit.
I will try another docking options i.e Patchdock and run MD afterwards.
Try to convert .pdbqt file to .pdb file using AutoDockTools. PDBQT files may have roots and branch information, which should be removed. PDBQT files also have charge and different atom type information than the PDB files. PyMOL cannot convert between these two file types efficiently. AutoDockTools can handle PDBQT files much better than any other program.
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