Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command and get the separate .top and .gro file for each chain using index file.
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