Thanks! This helps a lot
Nils Drechsel
On Thu, December 17, 2009 2:03 pm, case wrote:
> On Thu, Dec 17, 2009, Nils Jan Daniel Drechsel wrote:
>>
>> I am currently in the processing of implementing the generalized Born
>> method igb=5 into our molecular simulator, Adun.
>
>> case 6:
>> if ( strncmp(sType,"C1",2) &&
>> strncmp(sType,"C2",2) && strncmp (sType,"C3",2) )
>> dGBrad = 1.7;
>> else
>> dGBrad = 2.2;
>> break;
>>
>>
>> On the last lines (case 6), different radii are associated with
>> different types of carbon. However, C1, C2 & C3 are nowhere to be
>> found in the parameter and topology files and I expect their meaning
>> to be how many hydrogens are bound to it, or something like that.
>> Would one of the developers be so kind to elaborate this association?
>> it would be of great help.
>
> C1, C2, and C3 are united atom carbons (carbons with implicit hydrogens
> attached). That is why (a) they don't exist in any of the all-atom force
> fields; and (b) if found they would be assigned a larger radius than that
> used for all-atom carbons.
>
> So, for comparison to all atom calcs, you can ignore C1, C2, and C3 atom
> types. [I haven't kept up on how much has been done to check GB
> calculations
> with united atom force fields...that would be in Ray's bailiwick.]
>
> ....dac
>
>
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--
Nils Jan Daniel Drechsel
Computational Biochemistry and Biophysics Lab
Barcelona Biomedical Research Park
C/ Doctor Aiguader 88
08003 Barcelona (Spain)
+34 933 160 506
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Received on Fri Dec 18 2009 - 03:00:03 PST
