Jason,
Many thanks for this. Let me see if I understand the process you describe.
1. I need to run MMPBSA.py with an input file such as:
Input file for running PB and GB
&general
"-make-mdins",
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
Of course this doesn't work because -make-mdins is wrong. Can you please help with the syntax.
2. Assuming that all works, I should get a number of output files including _MMPBSA_pb.mdin. This I have to modify by including set npbopt=1.
3. Re-run MMPBSA.py using the same input file as in step 1 with the modification that instead of -make-mdins, I use -use-mdins.
4. Repeat step 3 above with different saltcon values.
Is this process what you suggested?
I also have a general questions. Forgive my ignorance as I am a novice. What is the difference between PBSA in AmberTools and MMPBSA.py?
Your help is greatly appreciated
George
On Aug 11, 2011, at 5:13 AM, Jason Swails wrote:
> On Wed, Aug 10, 2011 at 7:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Jason,
>>
>> Thank you. Due to oversight I did not attach the script. I'm copying it
>> below for easy reference. Is there something more that I should do under
>> &pb? Can I use saltcon=x.xxx under &pb as well?
>>
>
> istrng is PB's version of saltcon (ionic strength vs. salt concentration).
> If you want to use the non-linear PB equation, you will need to run MMPBSA
> with the -make-mdins flag, modify the _MMPBSA_pb.mdin file to use the
> non-linear equation (set npbopt=1), then re-run MMPBSA with the -use-mdins
> flag to make sure it reads in your modifications. Note that you need every
> command-line flag present for each MMPBSA command (the first to create the
> input files and the second to use the modified ones).
>
> HTH,
> Jason
>
>
>> Thanks in advance
>>
>> George
>>
>> Input file for running PB and GB
>> &general
>> endframe=50, verbose=1,
>> # entropy=1,
>> /
>> &gb
>> igb=2, saltcon=0.100
>> /
>> &pb
>> istrng=0.100,
>> /
>>
>> On Aug 10, 2011, at 11:04 PM, Jason Swails wrote:
>>
>>> If you really want to analyze salt effects, you should use the nonlinear
>> PB
>>> equation rather than GB, as it provides a better approximation.
>>>
>>> HTH,
>>> Jason
>>>
>>> On Wed, Aug 10, 2011 at 9:26 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>
>>>> I'm trying to analyse the effect of ionic strength on the Delta G of
>>>> binding of a protein-ligand complex.
>>>>
>>>> I've been trying to do this by changing saltcon in the script below from
>>>> 0.1 through to 0.8. I've observed little or no difference which does
>> not
>>>> much experimental data.
>>>>
>>>> Is there something else I should be doing? Your advice will be much
>>>> appreciated.
>>>>
>>>> Regards
>>>>
>>>> George
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Aug 11 2011 - 04:30:02 PDT
