Hi, I'm doing a simulation of an organic compound containing an iodine
atom bonded to an aromatic ring.
The molecular dynamics simulation using pmemd.cuda was successful, as
was the gbsa and pbsa calculations.
However, the gbsa decomp calculation fails with the following message:
bad atom type: i
This error has been reported before, and it seems it's a problem with
the vdw data missing for iodine.
http://archive.ambermd.org/201412/0132.html
http://structbio.vanderbilt.edu/archives/amber-archive/2009/5852.php
Firstly, I'm quite surprised the gbsa calculation was successful since
as far as I can see, it also needs the vdw data for iodine. So, please
correct me if I'm mistaken, but the decomp should also work then, right?
Shouldn't the calculation take this data from the parameter file?
Secondly, could you please confirm if I have to modify the source code
and add the missing vdw data? If so, could you let me know where the
original data was taken from, so that I can use the same source?
Finally, if the vdw data is taken from that source code file, can't we
use different radii sets for decomp calculations, as we use for gbsa
with the radii variable in ante-MMPBSA.py?
Thanks in advance for your help!
Regards,
Bruno
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Received on Thu Jun 30 2016 - 12:00:03 PDT
