Hello:
I am building a protein model using a script that has been cited several times.
http://salilab.org/modeller/wiki/Mutate%20model
I started to work on it using Modeller9v2 on a Windows XP machine. After some tries, I noted that I can use the script with the next command for example:
mod9v7 mutar.py 1dxt 85 TYR A
However, I needed to delete lines 2 and 165 of the script because the "import os" command is not recognized by the python version that is included with modeller.
The script seems to work and autogenerates a log file and the mutant model of course. I am working with a model of hemoglobin (1DXT). However, after looking the log file there some messages that are intriging for me:
a) Some atoms were not found in params file:
generat_607W> Cannot find params in params file: CHARMM atoms : NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B Atom indices : 4406 4405 4407 4414 Residues : HEME HEME HEME HEME
As this is hemoglobin model HEME groups are important
b) Serious non-bounded atoms contacts at the end of the script
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 650 4405 2.247 serious non-bonded atom clash: 1778 4448 2.197 serious non-bonded atom clash: 2850 4491 2.252 serious non-bonded atom clash: 3978 4534 2.101
c) The modelling was produced in few seconds. Can the model produced by this script be optimized even more? (even if the script takes more running time)
Also I am interested in create a mutant model but without optimize it. Then I want to compare the energy of the mutant model before and after the optimization.
How can I produce the mutant model without the optimization?
I am attaching the log file of my previous model.
Thanks
Dr. Alfonso Méndez Tenorio