On Sat, Mar 11, 2017, 鲁俊波 wrote:
>
> I run the hydration of Cu2+ as a testing for amber. I first do
> an energy minimization, but there is a problem when I use ambpdb
> command. I run the command:
>
> ambpdb -p cu.prmtop < cu_min.crd > cu_min_final.pdb
Try this: ambpdb -p cu.prmtop -c cu_min.crd > cu_min_final.pdb
If your cu_min.crd file is a binary done (i.e. if "file cu_min.crd" returns
DATA), you need the -c flag. (You seem to have attached all the files
*except* cu_min.crd....)
...hope this helps...dac
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Received on Mon Mar 13 2017 - 08:30:02 PDT
