On Fri, Aug 12, 2011, Charles Johnson wrote:
>
> I have been using leaprc.ff10. When I convert the pdb file generated in
> nab to an amber pdb with ambpdb I obtain a file that looks like this:
>
> ATOM 1 HO5' G5 1 3.429 -7.861 3.641 1.00 0.00
> ATOM 2 O5' G5 1 4.232 -7.360 3.480 1.00 0.00
> ATOM 3 C5' G5 1 5.480 -8.064 3.350 1.00 0.00
> ATOM 4 H5' G5 1 5.429 -8.766 2.518 1.00 0.00
> ATOM 5 H5'' G5 1 5.679 -8.609 4.273 1.00 0.00
>
> I have been told that the reside names are not in a correct AMBER
> format. Is this true or am I doing something incorrect here?
Looks fine to me. You might ask the person who complained to explain his or
her reasoning. Note that if you want things to look more like a PDB file,
consider using the "-bres" flag to ambpdb.
...dac
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Received on Sat Aug 13 2011 - 05:30:04 PDT
