On Wed, Feb 08, 2012, Olena Dobrovolska wrote:
> 1. I found that instead of hydrogens it puts oxygen atoms because there
> are no N-terminal H1, H2 and H3.
OK: you have to fix this, then re-run makeDIST_RST.
>
> 2. when opened amb file in xleap these atoms are added. but after the generation of parameter files, the command
>
> ambpdb -aatm -p prmtop < P1.x > P1.amb.pdb
>
> gives me an error message 'syntax error', thus, I can't save the pdb file.
Please update to the current version of AmberTools. Or, please post your
prmtop and P1.x files, and we'll try to figure out why ambpdb is failing.
You can also use savePdb inside LEaP to create a pdb file. (If you do wnat
to upload your files, please indicate which version of AmberTools you are
using.)
>
> 3. my RST file is right,
I don't agree: your RST file is wrong, since it was made with a bad pdb file.
...dac
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Received on Wed Feb 08 2012 - 11:00:03 PST
