Re: [modeller_usage] Conversion of L-isomers to their D-isomeric form
To: abdullah ahmed <>
Subject: Re: [modeller_usage] Conversion of L-isomers to their D-isomeric form
From: Modeller Caretaker <>
Date: Thu, 04 Feb 2010 16:38:16 -0800
Cc:
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.