| 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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