Re: [AMBER] bad atom type decomp

From: Bruno Falcone <>
Date: Fri, 1 Jul 2016 00:45:48 -0300 (ART)

Hi Hai, thanks for your reply.

I'm using fully updated Ambertools 15 and Amber 14.


> On Thu, Jun 30, 2016 at 2:33 PM, Bruno Falcone
> <>
> 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.
>> 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
> Hi,
> please give more detail about exact versions you are using too.
> cheers.
> Hai
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Jun 30 2016 - 21:00:02 PDT
Custom Search