From NWChem
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Just Got Here
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| 1:00:18 PM PST - Mon, Jan 23rd 2012 |
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Dear NWChem Users,
I am trying to generate topology file using pdb file. Total number of atoms is 40914 and residue is 12338 including protein, nucleic, ions and water. After resid 999 that is from resid 1000 to resid 1233 while I am generating topology file creates some error like "Coordinates missing for atom", but everything is correct, I checked with vmd for thsoe residues. Basically those are water, but for other waters work perfect. So why after resid 999 to resid 12333 creates problem. Please suggest any suggessions.
Could you please provide me information about each line of topology file, what exactly indicates, it will be great help for me.
Have a nice weekend,
Thanks,
Maiti
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| 3:59:05 PM PST - Mon, Jan 23rd 2012 |
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From the error message it appears that the prepare module did not find certain atoms in some of your residues. This is almost always a result of atoms names being different from the definitions in the NWChem database files. NWChem adheres strictly to the PDB atom naming convention.
Without access to your PDB file or the generated output file it is difficult to be more specific.
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 2
Posts 286
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| 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://www.nwchem-sw.org/index.php/Prepare for details).
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 2
Posts 286
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| 1:18:16 PM PST - Thu, Jan 26th 2012 |
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Additional info from NWChem MD developer Tjerk Straatsma:
Your PDB file had a number of small problems related to not following the PDB conventions. The attached PDB file has the corrections needed as follows:
1. The name of water as solvent is by default “HOH”. If you wish to use a different name, you need to specify this in your input or .nwchemrc file
2. The atom names for water are OW, 2HW and 3HW in the default HOH
3. The supplied segment files for Na and Cl ions are Na.sgm and Cl.sgm with atom names Na and Cl respectively. There is an exception to this for Mg, see point 4.
4. Because the standard AMBER database has MG as fragment name, a file MG.sgm is supplied, but the atom name is Mg.
After these edits in your pdf file, the prepare module is generating the topology and restart files.
Some additional comments:
1. Your ABS fragment/segment file does not contain appropriate charges. You will need to edit these files to supply the correct charges
2. All solvent molecules should have the same name. You were using WA1 and WAT. If this is to distinguish between crystal waters and added solvent you can do this by solvent molecule number. NWChem does not change this order!
3. Make sure that the overall charge of the system is what you intend it to be. The output file(s) give you all the information you need.
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