Without setting inp it takes npopt=1.
Norbert
Le 20/03/2015 17:21, Kenneth Huang a écrit :
> Norbert,
>
> Out of curiosity, have you tried running a trial run without setting inp,
> and just letting it default to 1? Likewise, do you have all the bugfixes
> applied?
>
> I'd also suggest trying it on AmberTools14 Or Amber12 for MMPBSA to see if
> it does run, unless you have a specific reason to not to.
>
> Best,
>
> Kenneth
>
> On Friday, March 20, 2015, Norbert GARNIER <norbert.garnier.cnrs-orleans.fr>
> wrote:
>
>> Dear amber list,
>>
>> I am using MMPBSA.py (amber11) to compute the binding free energy of a
>> (Protein-dna)-ligand complex
>> with /usr/local/amber11/src/mmpbsa_py/MMPBSA.PY
>> My input file is the following:
>>
>> &general
>> startframe=1, interval=50, endframe=5000, keep_files=2,
>> receptor_mask=':1-299', ligand_mask=':300',
>> strip_mdcrd=1, strip_mask=':Na+:ZNA',
>> /
>> &pb
>> istrng=0.000, exdi=80.0, indi=1.0,
>> inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
>> fillratio=4, scale=2.0,
>> linit=1000, prbrad=1.4, radiopt=1,
>> /
>>
>> I have the following message:
>> Warning: Input error! "inp=2" is an invalid option.
>>
>> Thank you very much for your help.
>>
>> Norbert
>>
>> --
>> Dr. Norbert GARNIER
>> Assistant Professor of physics - Orléans University
>>
>> « DNA repair: structural and functional approaches»
>> Centre de Biophysique Moléculaire, UPR4301, CNRS
>> Rue Charles Sadron
>> CS 80054
>> 45071 Orléans cedex 2
>> Tel: +33 (0)2 38 25 76 68
>> Web site : http://cbm.cnrs-orleans.fr/
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--
Dr. Norbert GARNIER
Assistant Professor of physics - Orléans University
« DNA repair: structural and functional approaches»
Centre de Biophysique Moléculaire, UPR4301, CNRS
Rue Charles Sadron
CS 80054
45071 Orléans cedex 2
Tel: +33 (0)2 38 25 76 68
Web site : http://cbm.cnrs-orleans.fr/
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Received on Fri Mar 20 2015 - 10:30:02 PDT
