| 10:59:35 AM PST - Thu, Jan 26th 2012 |
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Posting private discussions on progress:
The issue does lie with your PDB file. After some pretty extensive analysis, it turns out that your PDB file does not adhere to the proper format as outlined on wwpdb.org.
The issue lies with the residue sequence number. That is fitted in colums 23-26 (i.e. an integer of length 4). So, this becomes a problem after water # 9999, as the number 10000 and beyond show up from colums 23 -27 (where column 27 is used for something else) and the residue sequence number is read incorrectly. I don’t see an easy way to fix this.
The only suggestion I can give is to remove the waters and use the “solvent” and solvate” keywords to add the water molecules (see http://nwchemgit.github.io/index.php/Prepare for details).
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