[gmx-developers] Error in handling mulptiple terminii in pdb2gmx

[Brian Smith]

When assigning terminii types in pdb2gmx (ie. NH3+, COO- etc) only the last
choice is applied to multiple chains.

Thus, for example, the insulin dimer has two disulphide linked chains (pdb
code 1AF7), and therefore two N-terminii and two C-terminii. It's not
inconcievable that the N-terminii are not necessarily the same (eg. one
chain could be N-terminal acetylated, while the other is charged NH3+).
While the user can select different terminii types within pdb2gmx, only the
last choice is applied. Thus, choosing '1' == NH3+ for the first chain, and
'0' == none for the second will only apply the last choice (none) to both
chains.

Inspection of the code for pdb2gmx indicates that the variables sel_ctdb and
sel_ntdb are not arrays ie. can handle only one case - the last choice.

Kind regards,...

Brian.

Dr Brian J Smith
The Walter & Eliza Hall Institute of medical research