> I tried to use xleap (amber8) to read in the structure of NADH, add hydrogens
> and save it as a PDB file for some simulation. Xleap read in the structure
> without any problem but when I used "savepdb" to save the structure, it gave the
> following message
>
> Non-[HED] atom name (NC1') too long for PDB standard - TRIMMING LAST CHARACTER
> Non-[HED] atom name (NH1') too long for PDB standard - TRIMMING LAST CHARACTER
> Non-[HED] atom name (NC2') too long for PDB standard - TRIMMING LAST CHARACTER
> ...
>
> which trimed some of the 4 letter atom names. My initial NADH pdb is as the
> following
>
> ...
> ATOM 5576 NN1 NAD 600 11.897 49.233 20.260 1.00 23.82
> ATOM 5577 NC1' NAD 600 12.002 47.794 20.133 1.00 23.51
> ATOM 5579 NC2' NAD 600 11.045 46.903 20.882 1.00 24.23
> ..........................
> .........................
I've never used NADH, but it seems to me that the 'N' that begins
each atom name should be eliminated. Only H's are supposed to be
4 chars long as far as I can remember.
Bill
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Received on Wed May 31 2006 - 00:11:59 PDT
