> On Jun 13, 2014, at 5:50 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com> wrote:
>
> Dear Prof Monard,
>
> Many thanks for your quick response, still I am unable to find any
> keyword that handles the optimizing process in sander. I went through the
> manual bt I was unable to find such keyword. I will deeply appreciate you
> if you help me to handle this process so that I can get proper QM
> optimization.
> Thanking you again.
What you're looking for is a basic minimization. Look at the imin and ntmin flags.
HTH,
Jason
>
>
>
> On Fri, Jun 13, 2014 at 12:31 PM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> Hi,
>>
>> You cannot use the Gaussian optimizer since it is sander that masters
>> what happens to the coordinates (from a coordinate set, sander asks
>> gaussian to compute an energy, it does not let gaussian modify them,
>> hence the "force" keyword).
>> You'd better use one of the optimizers available in sander (&cntrl
>> namelist) instead.
>>
>> Gerald.
>>
>>
>>> On 06/13/2014 11:16 AM, Kshatresh Dutta Dubey wrote:
>>> Dear Users
>>>
>>> I am using Amber 14 for QM/MM calculation with Gaussian as external
>>> interface. I have to optimize a system containing some amino acids and a
>>> ligand in QM regions. I found that Amber automatically adds some keywords
>>> in route section of Gaussian input that force Gaussian to do single point
>>> calculations. For example, I used :
>>> *&gau*
>>> * mem = '2GB'*
>>> *! method = 'B3LYP',*
>>> *! basis = '6-31G',*
>>> * use_template =1,*
>>> * num_threads = 2*
>>> * /*
>>> for &gau namelist and :
>>>
>>> *#P OPT B3LYP/6-31G SCF=(Conver=8)*
>>>
>>> for template file namelist. The calculations runs fine and it shows
>> normal
>>> termination, but I found that it does only single point calculation not
>>> optimizing the structure while I have mentioned optimization in route
>>> sections. I notice that Amber adds some additional keyword such as
>> 'Force'
>>> in route section which restricts Gaussian to calculate forces only. I
>> guess
>>> it is fine for QM-MM/MD since we need forces for dynamics, but here I am
>>> interested in QM/MM optimization only. The route section modified by
>> Amber
>>> is :
>>>
>>> *#P OPT B3LYP/6-31G SCF=(Conver=8) NoSymm Force Guess=Read Charge Prop=*
>>> * (Field,Read)*
>>>
>>> How can I disable 'Force' keyword so that I can perform proper
>>> optimization. I will be thankful for your help.
>>>
>>> thanks
>>
>> --
>>
>> ____________________________________________________________________________
>>
>> Prof. Gerald MONARD
>> SRSMC, Université de Lorraine, CNRS
>> Boulevard des Aiguillettes B.P. 70239
>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>
>> e-mail : Gerald.Monard.univ-lorraine.fr
>> tel. : +33 (0)383.684.381
>> fax : +33 (0)383.684.371
>> web : http://www.monard.info
>>
>>
>> ____________________________________________________________________________
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> With best regards
> ************************************************************************************************
> Dr. Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> c/o Prof Sason Shaik,
> Hebrew University of Jerusalem, Israel
> Jerusalem, Israel
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 13 2014 - 04:00:02 PDT
