On Fri, Apr 4, 2014 at 7:25 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
>
> On Fri, Apr 4, 2014 at 5:55 PM, Manikanthan Bhavaraju <
> manikanthanbhavaraju.gmail.com> wrote:
>
>> Hi Jason,
>>
>> Thanks for replying. Yes, it is line 2125. The lines 2078 to 2085 is:
>>
>> else
>> ! write( 0,* ) 'bad atom type: ',atype
>> ! call mexit( 6,1 )
>> x(l165-1+i) = 1.70 + 1.4;
>> x(l170-1+i) = 0.51245;
>> x(l175-1+i) = -0.15966;
>> x(l180-1+i) = -0.00019781;
>> x(l185-1+i) = 0.00016392;
>>
>> As per your suggestion I can use a similar format for the Ca+2 ion after
>> line 2125
>>
>> else
>> !write( 0,* ) 'bad atom type: ',atype
>> !call mexit( 6,1 )
>> x(I165-1+i) = 1.33 + 1.4;
>> x(l170-1+i) = ??;
>> x(l175-1+i) = ??;
>> x(l180-1+i) = ??;
>> x(l185-1+i) = ??;
>>
>> Then, what about the values for other lines? I mean x(I170-1+i),
>> x(I175-1+i), and so on. How to define these values? Can you please
>> explain
>> a bit about them?
>>
>
> Those are LCPO parameters. If you look below (line 2393) it says
>
! dummy LCPO values:
x(L170-1+i) = 0.0d0
x(L175-1+i) = 0.0d0
x(L180-1+i) = 0.0d0
x(L185-1+i) = 0.0d0
They're unused for gbsa=2, so you can keep them all set to 0.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 04 2014 - 16:30:02 PDT
