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I have taken 4INS, pdb file, for insulin peptide. There are two chains linked by disulfide bonds. While I have created the topology file for this peptide both A and B chains are interconnected at residue 7 and residue 8 respectively and the rest part of the B chain is missing from the protein file. Please suggest the solution in which I could do this.
Here I have attached the snapshot of both original pdb file (red color) and the peptide file (blue color) after topology creation.
Sorry I do not fully understand your questions? Do you want to know how to define S-S bond between 2 chains using pdb2gmx? Or do you ask how to add residues to your pdb file?
Thanks
\Alessandra
Dear mam,
After creating the topology file, the A chain (21AAs) connected to the B chain (30AAs) at residue number 7. So, the rest residues of the B chain are not shown in VMD.
Kindly tell me how to get the correct conformation of both chains.
Hi,
VMD is reading pdb or gro files, not topology files. It may be a problem of visualization style. You can try to visualize using the opition style “lines” (for example), you might see all the atoms belonging to the two chains.
I saw that atom 7 is CYS, is this residue involved with S-S bridge with the other chain? Then cross check that the S-S bridge is properly recognized by pdb2gmx (-merge all and -ss may be options to be considered).
\Alessandra
Hi,
If you have S-S bridge between two chains, use the option -merge and -ss to generate the topology. For the visualization with VMD, cartoon-style may not work (it will not shown the whole system)
Alessandra
