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Making Disulfide BondsTable of contentsNo headersThe easiest way to do this is by using the mechanism implemented with the specbond.dat file and pdb2gmx. You may find pdb2gmx -ss yes is useful. The sulfur atoms will need to be in the same unit that pdb2gmx is converting to a moleculetype, so invoking pdb2gmx -chainsep correctly may be required. See pdb2gmx -h. This requires that the two sulfur atoms be within a distance + tolerance (usually 10%) in order to be recognised as a disulfide. If your sulfur atoms are not this close, then either you can
Otherwise, editing your .top file by hand is the only option. |