On Thu, Jun 30, 2016 at 2:33 PM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
wrote:
> 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?
>
>
Hi,
please give more detail about exact versions you are using too.
cheers.
Hai
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 30 2016 - 19:30:02 PDT
