Hello all,
We need to iterate in and out of a PDB file during refinement, which requires that ambpdb generate a PDB file identical in format to that input to tleap via loadPDB. The process is failing, owing to the fact that ambpdb isn't writing the different chain IDs.
I gather this should be possible with the -ext option to ambpdb, but this gives "PRMTOP file did not have extended PDB data". I presume that there must be some option to loadPDB to preserve the chain assignments, and/or an option to saveamberparm to write the "extended PDB data" to the prmtop file.
I've combed the documentation, and a fair fraction of the web, in vain. Could anybody *please* enlighten me?
Many thanks,
John
---------------------------------------
John Gehman
ARC Future Fellow
School of Chemistry
Bio21 Institute
Univ. of Melbourne VIC 3010
+61 3 8344 2417
http://www.gehmanlab.com
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Received on Sun Aug 04 2013 - 15:30:02 PDT
