[gmx-developers] Error in handling mulptiple terminii in pdb2gmx
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 21 13:53:39 CET 2002
On Thu, 21 Feb 2002, Brian Smith wrote:
>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
>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.
pdb2gmx only recognizes chains if they are labeled with the normal pdb
label (A,B etc). If that is the case each chain is treated indepently and
you can select the N- and C- terminus independently.
However one of the remaining problems in pdb2gmx is to create disulphides
(and generally interactions) between multiple chains.
By the way, it seems that 1AF7 is not insulin:
COMPND 2 MOLECULE: CHEMOTAXIS RECEPTOR METHYLTRANSFERASE CHER;
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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