Thank you. I did that but I obtained the same error.
I also extracted the pdb file from frame 1 of the trajectory without
solvent to see if the residue numbers are correct and indeed they match
those in the top file of the complex. Does anyone has other suggestion
about what may be wrong?
I am using AmberTools12.
Em 2014-02-24 13:13, Jason Swails escreveu:
> On Mon, 2014-02-24 at 11:31 +0000, almarques wrote:
>> Hi,
>>
>> I have bee trying to run the mmpbsa.py for alanine scanning
>> mutagenesis
>> but I always get this error:
>>
>> Loading and checking parameter files for compatibility...
>> PrmtopError: Couldn't predict mask from topology files!
>> Your ligand residues must be sequential in your complex.
>> There are likely problems with your topology files if this is not the
>> case.
>>
>> My input is:
>>
>> sample input file for running alanine scanning
>> &general
>> startframe=3000, endframe=5000, interval=1000,
>> verbose=1,
>> ligand_mask=':1-200,806,810',
>> receptor_mask=':201-401,402-603,604-805,807,808,809,811,812,813',
>
> Consider simplifying your receptor mask to ':201-805,807-809,811-813'
>
> Also, it would help to know what version of AmberTools you are using.
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Received on Mon Feb 24 2014 - 06:30:02 PST
