On 02/04/2010 09:07 AM, abdullah ahmed wrote: > 1. Making a series of models rather than just one to avoid problems > caused by randomization. > 2. Turning randomization off using the "deviation=None" command in > the "allhmodel" parameters.
deviation=None selects the default, which is 4 angstroms I believe. To get no deviation, use deviation=0.
> 4. Finally I tried using 2 files from the RCSB protein data bank, > with post numeration (ie atoms are labelled HD1 rather than 1HD). > This was to check if the error was from my PDB file.
Modeller will still build models if your input PDBs do not have correct atom naming; it just will not use the coordinates of the incorrect template atoms, and instead generate them from internal coordinates (HD1 is the correct name for remediated PDB).
> 5. Finally, I get these warnings in the ".log" file: > > * mdtrsr__446W>..... > * getf__W> RTF restraint not found > * iup2crm_279W> IUPAC atom not found in topology library
Please quote the full warning message - it's impossible to tell what the problem is from just a snippet.
Ben Webb, Modeller Caretaker