Topology
Just Got Here
6:58:38 PM PST - Mon, Jan 23rd 2012
Dear Nwchem Users,

Thank you very much for your kind reply. Now I am sending more clear email that way it will be easy for you to understand my question and it will solve my problem.

My initial (input) PDB file was made from different PDB files contain protein, nucleic, ions and waters. So the atom and residue numbers of input PDB file are not ordered. So my question is tha t: when I tried to generate the seg, frg, top and rst files, is Nwchem reordering the atom and residue numbers of input PDB file (not ordered) before generating the seg, frg, top and rst files.

Also could you please send me some notes about indicating of the each line of topology file as I not getting in manual.

Could you please send me reply, it will be great help for me.

Have a nice day,
Thanks again,
Maiti

  • Guest -
11:42:38 AM PST - Wed, Jan 25th 2012
We would be happy to help diagnose your problem, but we need access to your pdb file to do so.

Forum Vet
10:59:02 AM PST - Thu, Jan 26th 2012
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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