Dear Amber community members, Bill, Jim and Ross,
Thanks for that suggestion, I just closed a few windows on my Linux PC
and reran the job and it got completed as shown in the bottom of this
message.
The difference between gb and pb results is large (-42.0688 and
-25.3752). What is the significance of this difference? The manual
suggests many references, could you suggest some imp. references where
I can get proper comparision of the two methods.
Is this result sufficiently rigorous for a publication purpose or
should I calculate the entropy factor as well using the tutorial
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm
After doing so how do I make use of DELTA S and DELTA G values to get
a more realistic picture.
Actually I have a series of ligands (some with similar structure and
some from other series) for my target for which I want to compare
binding free energies, docking results and known IC50 values.
Your comments and suggestions will be valuable for my work as earlier.
Waiting for the same...
Thanks once again.
On Sun, Jun 6, 2010 at 4:45 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You are running out of available memory to perform the PB calculation. I
> would suggest you increase the amount of memory allocated to this
> calculation. If this is not a possibility for you, then you can decrease
> 'fillratio' from 4 (default) to 2 which will utilize less memory, but this
> may cause a different error during the ligand PB calculation.
>
> Good luck!
>
> -Bill
>
>
> On Sun, Jun 6, 2010 at 5:37 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
>
>> Dear Amber community members, Bill, Jimm and Ross,
>> Thanks for your inputs and suggestions.
>>
>> I have rerun the job in another folder.
>> The gb calculation is running ok and only gb results are written to the
>> FINAL_RESULTS_MMPBSA.dat files and corresponding mdout files are also ok.
>> But there is follwoing error in the _MMPBSA_complex_pb.mdout and
>> _MMPBSA_receptor_pb.mdout files. This error is not seen in the
>> _MMPBSA_ligand_pb.mdout file. (please check the attached files).
>>
>> I'm unable to understand what this error means. Please find time and see
>> if you can suggest some solution to the problem.
>> --------
>> POST-PROCESSING OF TRAJECTORY ENERGIES
>> trajectory generated by
>> ptraj
>> minimizing coord set # 1
>> SA Bomb in sa_arc(): Allocation aborted 0 210 210 0 0
>> ----------------
>>
>>
>> On 6/5/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>>
>>> What is in your _MMPBSA_complex_pb.mdout, _MMPBSA_receptor_pb.mdout, and
>>> _MMPBSA_ligand_pb.mdout? If there is something going wrong with the PB
>>> calculation, the error message will most likely be in one of these files
>>> when you are running the PB calculation. Take a look at these files and see
>>> if you can find the error, or at least something that will point to the
>>> error.
>>>
>>> Good luck!
>>>
>>> -Bill
>>>
>>>
>>> On Sat, Jun 5, 2010 at 1:25 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
>>>
>>>> Dear Amber community members, Bill, Jim and Ross,
>>>> Thanks for your comments and suggestions on MMPBSA earlier,
>>>> After solving the receptor and ligand mask issue, I was getting "No
>>>> potential terms in sander output error"
>>>>
>>>> I doubt that the prmtop file is an issue here because when I'm adjusting
>>>> the input for doing only gb calculation, it is working properly and giving
>>>>
>>>> DELTA G binding = -42.0688 +/- 3.4141
>>>> 0.4828 (please check the attached file)
>>>>
>>>> So there is a problem with the pb calculation. If I'm correct here,
>>>> could you please point to what is going wrong in the pb calculation and how
>>>> to fix that?
>>>>
>>>> Input file:
>>>> |--------------------------------------------------------------
>>>> |Input file for running PB and GB in serial
>>>> |&general
>>>> | endframe=50, keep_files=2,
>>>> | receptor_mask=:1-271:272-284, ligand_mask=:285
>>>> |/
>>>> |&gb
>>>> | igb=2, saltcon=0.100,
>>>> |/
>>>> |--------------------------------------------------------------
>>>> |Solvated complex topology file: 2PRG_rosi_solvated.prmtop
>>>> |Complex topology file: 2PRG_rosi_NW.prmtop
>>>> |Receptor topology file: res.prmtop
>>>> |Ligand topology file: rosi.prmtop
>>>> |Initial mdcrd(s): rosi_MD_1ns.mdcrd
>>>>
>>>> |Calculations performed using 50 frames.
>>>> |
>>>> |All units are reported in kcal/mole.
>>>>
>>>> -------------------------------------------------------------------------------
>>>> On 6/2/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>>>>
>>>>> Your ligand is just one residue, right? If this is the case, then
>>>>> MMPBSA.py should be able to guess the receptor_mask and ligand_mask without
>>>>> you specifying it. If MMPBSA.py cannot guess the masks with a one residue
>>>>> ligand, then more than likely there is an inconsistency with the prmtop
>>>>> files.
>>>>>
>>>>> The error that you are now getting means that the sander calculations
>>>>> (GB and PB) did not actually calculate any energies. The reason for this
>>>>> error is probably a sander error that should be near the end of the
>>>>> _MMPBSA_*.mdout files. This should have a sander error message that will be
>>>>> helpful. You also might want to check the STDOUT and STDERR files for any
>>>>> possibly important messages that got printed there.
>>>>>
>>>>> Good luck!
>>>>>
>>>>> -Bill
>>>>>
>>>>>
>>>>> On Wed, Jun 2, 2010 at 6:37 AM, vaibhav dixit <vaibhavadixit.gmail.com
>>>>> > wrote:
>>>>>
>>>>>> Dear Amber community member,
>>>>>> Thanks for your suggestions earlier.
>>>>>> I have tried to fix the receptor and ligand masking issue as specified
>>>>>> in the mail below. Please check if thats ok.
>>>>>>
>>>>>> But now I'm getting another error as follows. I'm not able to
>>>>>> understand what is this potential terms error in sander output. I have
>>>>>> attached my initial and avgcomplex pdb files here, but can't attach the
>>>>>> mdcrd file as it makes the message large and is not delivered.
>>>>>>
>>>>>> Please find time and see if you can suggest some solution to the
>>>>>> issue.
>>>>>>
>>>>>> The ERROR is given below.
>>>>>> ---------------------------------------------
>>>>>> [vaibhav.localhost MMPBSA]$ pwd
>>>>>> /home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
>>>>>> [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
>>>>>> mmpbsa_2b.in FINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop
>>>>>> -cp 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
>>>>>> ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
>>>>>> sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
>>>>>> only!)
>>>>>> Assuming /home/vaibhav/software/amber10/exe/sander is part of
>>>>>> amber9 or amber10. Using old PB input file.
>>>>>> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
>>>>>> modified Bondi radii (mbondi)
>>>>>>
>>>>>> Preparing trajectories with ptraj...
>>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>>
>>>>>> Starting sander calls
>>>>>>
>>>>>> Starting gb calculation...
>>>>>>
>>>>>> Starting pb calculation...
>>>>>>
>>>>>> Error: No potential terms in sander output! Check output files.
>>>>>> NOTE: All files have been retained for debugging purposes. Type
>>>>>> MMPBSA.py --clean to erase these files.
>>>>>> [vaibhav.localhost MMPBSA]$
>>>>>> ---------------------------------------------
>>>>>>
>>>>>> On 6/2/10, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
>>>>>>>
>>>>>>> Dear Amber community members,
>>>>>>> Thanks Bill for your comments.
>>>>>>> Based on your suggestion I have given the receptor and ligand mask in
>>>>>>> the following way.
>>>>>>> My pdb file with receptor and ligand, mmpbsa.in and the prmtop files
>>>>>>> are attached with this mail.
>>>>>>>
>>>>>>> (there are two chain of protein residue 207-477 and 608-627) I have
>>>>>>> counted them as receptor_mask=:1-271:272-284, ligand_mask=:285
>>>>>>>
>>>>>>> Please check wheather this assignment is correct or not?
>>>>>>> Thanks once again for your inputs and suggestions.
>>>>>>> ---------------------
>>>>>>> Input file for running PB and GB in serial
>>>>>>> &general
>>>>>>> endframe=50, keep_files=2,
>>>>>>> receptor_mask=:1-271:272-284, ligand_mask=:285
>>>>>>> /
>>>>>>> &gb
>>>>>>> igb=2, saltcon=0.100,
>>>>>>> /
>>>>>>> &pb
>>>>>>> istrng=0.100,
>>>>>>> /
>>>>>>> ------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> On 6/1/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>>>>>>>
>>>>>>>> Did you specify the receptor_mask and ligand_mask variables in your
>>>>>>>> input
>>>>>>>> file? MMPBSA.py has a built in function to determine which residues
>>>>>>>> correspond to the receptor and which residues correspond to the
>>>>>>>> ligand.
>>>>>>>> However, the guesser only works if all of the ligand residues are
>>>>>>>> sequential
>>>>>>>> (one after the other with no receptor residues in between). If this
>>>>>>>> is not
>>>>>>>> the case in your system, then you will need to specify receptor_mask
>>>>>>>> and
>>>>>>>> ligand_mask in the &general section of the MMPBSA.py input file.
>>>>>>>> Otherwise,
>>>>>>>> the guesser should work just fine, and if it isn't there might be an
>>>>>>>> inconsistency with the prmtops that you provided.
>>>>>>>>
>>>>>>>> I hope that helps explain things a little better.
>>>>>>>>
>>>>>>>> -Bill
>>>>>>>>
>>>>>>>> On Tue, Jun 1, 2010 at 10:46 AM, vaibhav dixit <
>>>>>>>> vaibhavadixit.gmail.com>wrote:
>>>>>>>>
>>>>>>>> > Dear Amber community members,
>>>>>>>>
>>>>>>>> > Thanks Jason for a prompt help with the tutorial. I could use the
>>>>>>>> new file
>>>>>>>> > successfully.
>>>>>>>> >
>>>>>>>> > I'm now trying the same tutorial procedure on my target protein
>>>>>>>> and ligand.
>>>>>>>> > Here I'm getting a different kind of error which is given below. I
>>>>>>>> could
>>>>>>>> > not
>>>>>>>> > understand what it exactly means and how could I fix it.
>>>>>>>> >
>>>>>>>> > Please find time and see if you could help me with same.
>>>>>>>> >
>>>>>>>> > The error is as follows:
>>>>>>>> > ---------------
>>>>>>>> > [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
>>>>>>>>
>>>>>>>> > mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop
>>>>>>>> -cp
>>>>>>>>
>>>>>>>> > 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y
>>>>>>>> *.mdcrd
>>>>>>>> > ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
>>>>>>>> > sander found! Using /home/vaibhav/software/amber10/exe/sander
>>>>>>>> (serial
>>>>>>>> > only!)
>>>>>>>> > Assuming /home/vaibhav/software/amber10/exe/sander is part of
>>>>>>>> > amber9 or amber10. Using old PB input file.
>>>>>>>> > Error: Could not predict mask from topology files! Make sure
>>>>>>>> ligand
>>>>>>>> > residues
>>>>>>>> > are
>>>>>>>> > sequential or specify receptor_mask and ligand_mask in the input
>>>>>>>> file.
>>>>>>>> > NOTE: All files have been retained for debugging purposes. Type
>>>>>>>> MMPBSA.py
>>>>>>>> > --clean to erase these files.
>>>>>>>> > [vaibhav.localhost MMPBSA]$ pwd
>>>>>>>> > /home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
>>>>>>>> > [vaibhav.localhost MMPBSA]$
>>>>>>>> > -------------------------------------------
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> > With regards
>>>>>>>> >
>>>>>>>> > Vaibhav A. Dixit
>>>>>>>> > Ph.D. Scholar
>>>>>>>> > Department of Medicinal Chemistry
>>>>>>>> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>>>>> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>>>>> > Punjab -160 062 INDIA
>>>>>>>> > Phone (Mobile): +919915214408
>>>>>>>> > E-mail: vaibhavadixit.gmail.com
>>>>>>>> > www.niper.nic.in
>>>>>>>> > _______________________________________________
>>>>>>>> > AMBER mailing list
>>>>>>>> > AMBER.ambermd.org
>>>>>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>> >
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> Bill Miller III
>>>>>>>>
>>>>>>>> Quantum Theory Project,
>>>>>>>> University of Florida
>>>>>>>> Ph.D. Graduate Student
>>>>>>>>
>>>>>>>> 352-392-6715
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> With regards
>>>>>>>
>>>>>>> Vaibhav A. Dixit
>>>>>>> Ph.D. Scholar
>>>>>>> Department of Medicinal Chemistry
>>>>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>>>> Punjab -160 062 INDIA
>>>>>>> Phone (Mobile): +919915214408
>>>>>>> E-mail: vaibhavadixit.gmail.com
>>>>>>> www.niper.nic.in
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> With regards
>>>>>>
>>>>>> Vaibhav A. Dixit
>>>>>> Ph.D. Scholar
>>>>>> Department of Medicinal Chemistry
>>>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>>> Punjab -160 062 INDIA
>>>>>> Phone (Mobile): +919915214408
>>>>>> E-mail: vaibhavadixit.gmail.com
>>>>>> www.niper.nic.in
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Bill Miller III
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Graduate Student
>>>>> 352-392-6715
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> With regards
>>>>
>>>> Vaibhav A. Dixit
>>>> Ph.D. Scholar
>>>> Department of Medicinal Chemistry
>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>> Punjab -160 062 INDIA
>>>> Phone (Mobile): +919915214408
>>>> E-mail: vaibhavadixit.gmail.com
>>>> www.niper.nic.in
>>>
>>>
>>>
>>>
>>> --
>>> Bill Miller III
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-6715
>>>
>>
>>
>>
>> --
>> With regards
>>
>> Vaibhav A. Dixit
>> Ph.D. Scholar
>> Department of Medicinal Chemistry
>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>> Punjab -160 062 INDIA
>> Phone (Mobile): +919915214408
>> E-mail: vaibhavadixit.gmail.com
>> www.niper.nic.in
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Sun Jun 06 2010 - 22:30:04 PDT
