Thanks Jason,
I'm running AmberTools 1.4.
I'll upgrade and try once again.
Regards
George
On Aug 11, 2011, at 5:19 PM, Jason Swails wrote:
> Hi George,
>
> Are you running with AmberTools 1.5? If not, I would suggest upgrading and
> using a nab program specifically written for this (MMPBSA.py will use this
> by default instead of sander, which will run faster than sander and give the
> same results). Furthermore, I don't know if npbopt was implemented in
> earlier versions (PBSA experts will have to comment here).
>
> HTH,
> Jason
>
> On Thu, Aug 11, 2011 at 10:47 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> 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
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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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>> 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 - 08:30:04 PDT
