On Fri, Jul 25, 2014, Changqing Yan wrote:
>
> I suddenly found that a pdb file which I use ambpdb script to generate
> looks like this.
>
> ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 *C*
> ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 *1*
> ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 *2*
> ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00 *C*
This looks like output from an old version of AmberTools(?). The original
algorithm tried to determine the element from the atomic name. Now, atomic
numbers are stored in the prmtop file, and used to generate element names.
If at all possible, you should now be using AmberTools14.
If you have a non-standard residue, you can make up your own names, of course,
but it is often helpful to use the names assigned by the PDB, if those are
available. Names like "1HA" look like holdovers from the very old PDB
(version 2) way of writing PDB files. You may want to consider using names
like HA1 and HA2 instead.
....dac
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Received on Fri Jul 25 2014 - 04:30:03 PDT
