On Aug 9, 2013, at 12:33 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
> Thanks Bill, I tried changing from :* to :1-385, however I get the same error. Any ideas?
qm_residues does not take a mask. It takes a comma-delimited list of residue numbers or ranges. This is described in the manual.
Good luck,
Jason
>
> Also, thanks for your response and congrats on the Ph.D!
>
>
> -Hunter
>
> -----Original Message-----
>> From: Bill Miller III <brmilleriii.gmail.com>
>> Sent: Aug 9, 2013 12:56 PM
>> To: Hunter Brown <bassoongoon.earthlink.net>, AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] MMPBSA selection error
>>
>> You need to explicitly specify the residue numbers for the qm_residues variable. MMPBSA.py will not recognize an asterisk for all residues.
>>
>> -Bill
>>
>> On Aug 9, 2013, at 12:29 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
>>
>>> I have created my prmtops using ante-MMPBSA.py.
>>>
>>> When I try to run MMPBSA.py to get deltaG information associated with bonding, I get the following:
>>>
>>> SelectionError: Invalid selection! Integers expected.
>>> Exiting. All files have been retained.
>>>
>>>
>>> Here is my input file:
>>>
>>> Input file for running PB and GB
>>> &general
>>> startframe=0, endframe=50, verbose=1, interval=5,entropy=1,
>>> /
>>> &gb
>>> ifqnt=1, qm_residues=:*, qm_theory=AM1, qmcharge_com=-8, qmcharge_lig=4, qmcharge_rec=-12, igb=2, saltcon=0.100
>>> /
>>> &pb
>>> istrng=0.100,
>>> /
>>> END
>>>
>>>
>>> Is the problem with the salt concentration or ionic strength flags? Because I would think that those should be able to have non integer values.
>>>
>>>
>>>
>>> Thanks in advance!
>>>
>>> -Hunter
>>>
>>> Hunter Brown
>>> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
>>> University of New Mexico
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
> Hunter Brown
> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
> University of New Mexico
>
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Received on Fri Aug 09 2013 - 14:30:04 PDT
