Sounds to me like your trajectory and prmtop files are incompatible. Make sure you stripped ions from both your prmtop files AND your trajectories, or that you didn't strip ions from either.
> On Mar 4, 2016, at 4:00 AM, chemjxn <chemjxn.126.com> wrote:
>
> Hi Jason,
> I checked the mmpbsa.out and _MMPBSA_complex_gb.mdout.0 files. No error in these two files. In the _MMPBSA_complex_gb.mdout.0, some terms equal to '-nan'. The same problem is found in my complexes (about 4 complexes).
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> At 2016-03-03 19:52:59, "Jason Swails" <jason.swails.gmail.com> wrote:
>>> On Thu, Mar 3, 2016 at 3:10 AM, chemjxn <chemjxn.126.com> wrote:
>>>
>>> Hello,
>>> I calculated some complexes. Then I want to perform the MM-GB/SA
>>> calculation. When I perform "./gbsa.sh" order, it turns up the same error
>>> (shown in mmgbsa_error.jpg) for all my complexes. I don't know how to solve
>>> this problem. Please help me. Thank you very much.
>>
>> Were there any error messages printed in the output before the traceback
>> started? Look for an error message in _MMPBSA_complex_gb.mdout.0 and put
>> the error message in that file into Google to see if there are any
>> suggestions.
>>
>> HTH,
>> Jason
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> <mmpbsa.out>
> <_MMPBSA_complex_gb.mdout.0>
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Received on Fri Mar 04 2016 - 05:30:03 PST
