yes you should expect to change the PBradii for igb (not ig!) 2 or 5. with
5, I suggest mbondi2 radii. I have not used igb=2.
On Fri, Mar 20, 2009 at 1:36 PM, Rajesh Raju <
Rajesh.Raju.postgrad.manchester.ac.uk> wrote:
> Hi Carlos,
>
> Thank you very much. I meant GB solvation model. So, that means in order to
> use IG=2 or 5, do i need to modify parameter file with mbondi2 radii?
> Actually I used the default radii set up by Leap. Thanks for your kind
> advice.
> Thanking u
> Rajesh
>
> uoting "Carlos Simmerling" <carlos.simmerling.gmail.com>:
>
>
> do you mean igb, not ig? ig is for the random number generator, igb is for
>> the GB solvent model.
>> I suggest finding a study that worked well on a system similar to your for
>> similar goals, and use that as a guide. it will be very hard to jusify
>> your
>> choice to journal reviewers if you say "I chose this based on an email
>> list". check the peer-reviewed literature.
>>
>> having said that, here is some advice:
>> I suggest igb=5 along with mbondi2 radii, this has worked well for me.
>> and yes, the PBradii are also used for GB, so it is important to choose
>> the
>> one you want. different radii are best with different GB models, so again,
>> check the literature to see what has worked for others.
>>
>> On Fri, Mar 20, 2009 at 1:20 PM, Rajesh Raju <
>> Rajesh.Raju.postgrad.manchester.ac.uk> wrote:
>>
>> Hi,
>>>
>>> I want to do MMGBSA free enrgy decomposition and binding energy
>>> calculations for my protein-ligand system. Which IG option (IG=1, 2, 5 )
>>> should i use ? Can i use the same paramter file for IG=1 and IG =2 .
>>>
>>> I read somewhere inorder to use IG =2 I should use the leap command
>>>
>>> ''set default PBradii bondi'' when setting up the prmtop file? But I
>>> have
>>> dount that I am doing MMGBSA (not PBSA). So should I modify the prmtop
>>> file?
>>>
>>> Cheers
>>>
>>>
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>
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Received on Sun Mar 22 2009 - 01:09:21 PDT
