From NWChem
Viewed 230 times, With a total of 1 Posts
|
|
|
Just Got Here
Threads 4
Posts 4
|
|
| 7:27:09 PM PST - Tue, Jan 24th 2012 |
|
Dear Nwchem Users,
I am getting problem after resid 999. The problem is that “missing atom in residue 1000”. But pdb file I checked everything is fine. I wounder to know if nwchem code is restricted for resid 999 and do I need to recompile for more than 999 residue. Also if any limitation for atom numbers. If I recompile where do I need to increase the array size for resid and atom numbers inside the source code ( basically file name and variable name in the source core). I am posting message but I am not getting any reply. Could you please give me, it will be great help for me.
Have a nice day,
Thanks,
Maiti
|
|
|
|
|
|
|
| 10:57:58 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://www.nwchem-sw.org/index.php/Prepare for details).
Quote:Bmaiti Jan 25th 2:27 amDear Nwchem Users,
I am getting problem after resid 999. The problem is that “missing atom in residue 1000”. But pdb file I checked everything is fine. I wounder to know if nwchem code is restricted for resid 999 and do I need to recompile for more than 999 residue. Also if any limitation for atom numbers. If I recompile where do I need to increase the array size for resid and atom numbers inside the source code ( basically file name and variable name in the source core). I am posting message but I am not getting any reply. Could you please give me, it will be great help for me.
Have a nice day,
Thanks,
Maiti |
|
|
AWC's:
2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
