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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Received on Sun Mar 22 2009 - 01:09:18 PDT
