[AMBER] Converting rst to pdb

From: Corum, Katharine W <katharine-corum.uiowa.edu>
Date: Tue, 9 Aug 2016 21:01:58 +0000

Hi again,

I would like to convert my .rst file to a pdb file. I went through some of the archived emails and found many old emails with the same commands but they did not work for me. I am using Amber16 and AmberTools16. I first tried ambpdb.

$AMBERHOME/bin/ambpdb -p cram.prmtop <min_qmmm.rst> min_qmmm.rst.pdb
Error: Could not read restart atoms/time.

Next I tried the cpptraj command and also received an error.

$AMBERHOME/bin/cpptraj -p cram.prmtop -y min_qmmm.rst -x min_qmmm.rst.pdb
/home/katie/Documents/software/amber/amber16/bin/cpptraj: error while loading shared libraries: libsander.so: cannot open shared object file: No such file or directory

After seeing these commands in many archived emailed I am not sure why I can't get it to work. Thank you!

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Received on Tue Aug 09 2016 - 14:30:03 PDT
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