Hi Hai, thanks for your reply.
I'm using fully updated Ambertools 15 and Amber 14.
Cheers!
Bruno
> 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
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Received on Thu Jun 30 2016 - 21:00:02 PDT
