Hi, I was wondering if someone got a chance to look at my question.
Speficically, if I go the recompilation route, what vdw radius should I
use for iodine?
Regards,
Bruno
On 01/07/16 00:45, Bruno Falcone wrote:
> 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 Tue Jul 05 2016 - 07:30:02 PDT
