Thank you Jason,
I run
1. MMPBSA.py.MPI -O -i mmpbsa.in -make-mdins -o FINAL_RESULTS.dat -sp solvated_complex.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
This produces _MMPBSA_gb.mdin and _MMPBSA_pb.mdin. The latter is
File generated by MMPBSA.py
&cntrl
ntb=0, cut=999.0, ntpr=1, imin=5,
maxcyc=0, igb=10, ipb=1, inp=1,
/
&pb
dbfopt=1, epsin=1, epsout=80, istrng=800.0,
radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4,
/
2. I edited the _MMPBSA_pb.mdin by adding npbopt=1 at the control name list and rerun MMPBSA.py as above using -use instead of make-mdins
Although the program produced FINAL_RESULTS.dat it complained that "Cannot match namelist object name npbopt
namelist read: misplaced = sign"
3. I repeated step 2 above but instead of adding npbopt=1 at the control name list, I added it in the &pb name list.
I got "Error: No potential terms in sander output! Check output files."
Your advice on which of the above steps is right will be most helpful
Thanks
George
On Aug 11, 2011, at 3:30 PM, Jason Swails wrote:
> Hi George,
>
> My mistake. -make-mdins and -use-mdins are command-line flags -- NOT
> something that goes in the input file. I should have been clearer about
> that.
>
> On Thu, Aug 11, 2011 at 7:17 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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.
>>
>
> You should only see temporary input files created, that is _MMPBSA_gb.mdin
> and _MMPBSA_pb.mdin (and maybe one or 2 others).
>
>
>>
>> 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.
>>
>
> On the command-line.
>
>
>>
>> 4. Repeat step 3 above with different saltcon values.
>>
>> Is this process what you suggested?
>>
>
> If you want to compare different salt concentrations or ionic strengths.
>
>
>>
>> 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?
>>
>
> PBSA is the program written to actually solve the PB equation. MMPBSA.py is
> more or less of a glorified bookkeeper and organizer. It arranges all of
> the input files and data, sets up calculations, and calls different programs
> (one of them being PBSA for solving the PB equation) to actually run the
> calculation, then parses the output files at the end and calculates basic
> statistics of the resulting data.
>
> HTH,
> Jason
>
>
>>
>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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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Received on Thu Aug 11 2011 - 08:00:03 PDT
