Thanks Jason
Rami
On Feb 28, 2012, at 8:53 PM, Jason Swails wrote:
> Then GBSA is set to 2 by default (decomp requires gbsa=2). This has been
> addressed on the list before (you can probably google for it).
>
> The solution is to add a default radius or the "real" radius to
> $AMBERHOME/src/sander/mdread.f (look for the error message you're getting
> -- that will take you to the relevant part of the code). Once you add code
> to handle that atom, recompile sander and it should work.
>
> HTH,
> Jason
>
> On Tue, Feb 28, 2012 at 7:08 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
>
>> Hi Dwight,
>> No, gbsa=2 is not set, but, yes, I am doing energy decomposition.
>> Here is the input file:
>> Input file for running GB
>> &general
>> verbose=2, strip_mdcrd=1, strip_mask=":WAT",
>> entropy=0, startframe=62, endframe=10000, interval=62
>> /
>> &decomp
>> idecomp=2, dec_verbose=3,
>> /
>> &gb
>> igb=5, saltcon=0.150
>> /
>> &pb
>> istrng=0.150
>> /
>> &nmode
>> nmstartframe=8, nmendframe=160, nminterval=6,
>> maxcyc=50000, drms=0.0001, nmode_igb=1, nmode_istrng=0.1,
>> /
>>
>> Thanks for your help.
>> Rami
>>
>> On Feb 28, 2012, at 6:33 PM, Dwight McGee wrote:
>>
>>> Hi,
>>>
>>> Is gbsa=2 in your input? Are performing an energy decomposition
>> analysis?
>>>
>>> On Tue, Feb 28, 2012 at 5:59 PM, Osman, Roman <roman.osman.mssm.edu>
>> wrote:
>>>
>>>> Greetings,
>>>>
>>>> I am running an mmpbsa_py on a complex with a small molecule that
>> contains
>>>> Br.
>>>> I am getting this error:
>>>>
>>>> Beginning GB calculations with sander...
>>>> calculating complex contribution...
>>>> bad atom type: br
>>>>
>>>> I assume the error is because of the Br.
>>>> I would be grateful if you suggest how to fix this problem.
>>>> Thanks very much,
>>>>
>>>> Roman Osman
>>>>
>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> T. Dwight McGee Jr.
>>> Quantum Theory Project
>>> University of Florida
>>> Graduate Student
>>> dwight.mcgee.gmail.com
>>>
>>> "Problems cannot be solved at the same level of awareness that created
>>> them."
>>> Albert Einstein
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Feb 29 2012 - 09:30:02 PST
