Thank you Jason for the reply. I added the new residue to to titratable_residues.py but "cpinutil.py - - describe" still does not list it as titratable residue at the end. Is it the atom naming or the atom order in the residue that's causing the problem Why is not recognizing it as a residue ?
> On Aug 26, 2015, at 2:00 PM, amber-request.ambermd.org wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: mismatch base pair from nab (David A Case)
> 2. Re: how to add lipid (Bill Ross)
> 3. What is the best way to study a dynamics route of a molecule
> to enter a protein (Wenyu Qian)
> 4. cpin error (Arjun Sharma)
> 5. Re: Problem In Performing MMPBSA Calculation for System
> Containing Lipids (anilkumarsahoo.physics.iisc.ernet.in)
> 6. Re: closest command in cpptraj (Joseph Baker)
> 7. Re: What is the best way to study a dynamics route of a
> molecule to enter a protein (David A Case)
> 8. Re: Problem In Performing MMPBSA Calculation for System
> Containing Lipids (David A Case)
> 9. Re: Problem In Performing MMPBSA Calculation for System
> Containing Lipids (Jason Swails)
> 10. Re: cpin error (Jason Swails)
> 11. Re: how to add lipid (mohammad r)
> 12. Re: how to add lipid (mohammad r)
> 13. Re: closest command in cpptraj (Daniel Roe)
> 14. Re: Total interaction energy between monomeric units of a
> dimer (anu chandra)
> 15. Re: Total interaction energy between monomeric units of a
> dimer (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 25 Aug 2015 15:57:41 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] mismatch base pair from nab
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150825195741.GB6843.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
>> On Tue, Aug 25, 2015, Martina Devi wrote:
>>
>> I did not get any error message.The base which I did not edit can be viewed
>> in xleap The desired edited base which I want to load cannot be viewed in
>> xleap.
>
> Can you be more specific about what you mean by "cannot be viewed in xleap"?
> What were the exact commands you typed, and what was the exact response from
> the program?
>
> Don't restrict your reporting to what you think are "error messages". In
> order to help, we need to know everything that happened.
>
>>
>> What I did was I made two pdb files. Then I edited the required portion and
>> copied from the other pdb. Is this technique correct?
>
> Remember that you must remove any atoms in your modified residue that are not
> supposed to be there: all atoms present in the PDB file must also be in the
> library file for the modified residue.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 25 Aug 2015 13:13:22 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] how to add lipid
> To: mohammad r <mohammad.r0325.yahoo.com>, AMBER Mailing List
> <amber.ambermd.org>
> Message-ID: <s734gs5g0dglrsdlpf20yc13.1440533602375.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> Trial and error.. also note that the box will shrink with equilibration because there are vdw voids in the initial placement.
>
> You could equilibrate your box without lipid, then remove the water, place with packmol, and write a program to remove the overlapping waters (unless packmol will do it). Remember, the box will shrink after every substitution or addition owing to the vdw voids created.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/25/2015 3:43 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
> </div>Indeed I don't know how to generate a fixed box of water around the lipid-peptide which is generated by packmol.
>
>
>
> On Tuesday, August 25, 2015 2:58 PM, mohammad r <mohammad.r0325.yahoo.com> wrote:
>
>
> I found it. tleap cannot recognize the water molecules, because when I generated the pdb file consisting of the protein and the lipids around it by packmol then imported it to the tleap, it could read it and there I solvated my system by water with solvatebox command. But there I have a problem again, as I want to add specified amount of lipids to my system (e.g. 10mM) and I don't know the dimensions of my system till the last level and these dimensions are changed as I change the numbers of lipids surround the peptide in packmol ( because I use solvatebox command for solvating water), so I cannot specify how many lipids I have to add in packmol ( to reach the specified molarity).
>
>
>
> On Tuesday, August 25, 2015 1:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> Looks like it isn't a pdb file - how about pasting a few lines here.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/24/2015 11:14 PM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
> </div>the error is like this:
> Creating new UNIT for residue: CLA sequence: 7622
> Created a new atom named: CLA within residue: .R<CLA 7622>
> Creating new UNIT for residue: CLA sequence: 7623
> Created a new atom named: CLA within residue: .R<CLA 7623>
> total atoms in file: 22939
> Leap added 208 missing atoms according to residue templates:
> 208 H / lone pairs
> The file contained 22738 atoms not in residue templates
>
>
>
> On Tuesday, August 25, 2015 9:13 AM, mohammad r <mohammad.r0325.yahoo.com> wrote:
>
>
> Thank you Bill;
> Before I use the loadpdb, I load leaprc.ff14SB, frcmod.ionsjc_tip3p, leaprc.lipid14 force fields.I've read the leap tutorial but still I don't know which section you mean. Do you know any other turorials?Also, is there another way to generate the solvated system except packmol? Maybe it would help.
> Best, M.
>
>
>
>
> On Monday, August 24, 2015 11:50 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> So you have to find or build residue templates and load them before loadpdb. Have you studied the tutorials yet? They are good for this. By now you should also have found papers by people who have done this in Amber to get the parameters at least.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/24/2015 10:44 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
> </div>No it cannot recognize the residues in the pdb file
>
>
> On Monday, August 24, 2015 10:11 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Mon, Aug 24, 2015 at 1:28 PM, mohammad r <mohammad.r0325.yahoo.com>
> wrote:
>
>> I tried loadpdb, but it couldnot read it.
>
> ?Is it a PDB file?? If loadPDB doesn't read it, there is probably
> something wrong with the PDB file and it violates the PDB standard in some
> way.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 25 Aug 2015 16:04:08 -0600
> From: Wenyu Qian <qianwenyu01.gmail.com>
> Subject: [AMBER] What is the best way to study a dynamics route of a
> molecule to enter a protein
> To: amber.ambermd.org
> Message-ID:
> <CA+aasP0_yWcF=CvugkzjQXWdX+g6A15dbqqNsKdGAW0N=OiSMg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello all,
>
> I have a protein with an empty pocket. I want to calculate the free energy
> of insertion of a molecule from solution to that pocket. I have a sort of
> idea on the pathway it should take.
>
> I think I can do this with umbrella sampling, but I am not sure how to. I
> viewed the tutorial about umbrella sampling, but it was only about
> conformational change.
>
> Is there anything you recommend that is similar to what I want to do?
>
> Best regards,
> Wenyu "Mac" Qian
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 25 Aug 2015 18:45:04 -0500
> From: Arjun Sharma <arjunsharma83.gmail.com>
> Subject: [AMBER] cpin error
> To: amber.ambermd.org
> Message-ID: <BA19CEFF-0A54-4DEC-B7D3-539A977AFC2B.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Dear Jason,
>
> I?m trying out a simple organic molecule for the explicit solvent CpHMD simulation.
>
> H-O=C-O
> |
> CH3-C-CH3
> |
> CH3
>
> I used partial charges from OPLS and calculated the reference energy for the deprotonated form with sander TI method (IGB 2). I added this molecule to the residue list in Cpinutil.py and Residues.py (in cpinutils dir) as per AMBER 15 manual.
> ----------------------------------------------------------------------------------------------------------
> Cpinutil.py :
>
> LINE 257: change(parm, 'RADII', ':PTN.O=,.OZ=', 1.3).execute()
> -------------------------------------------------------------------------------------------
> Residue.py:
>
> # PTN
> refene1 = _ReferenceEnergy(igb2=0)
> refene1.solvent_energies()
> refene1.dielc2_energies(igb2=0)
> refene1.dielc2.solvent_energies()
> refene2 = _ReferenceEnergy(igb2=-44.8284)
> refene2.solvent_energies()
> refene2.dielc2_energies()
> refene2.dielc2.solvent_energies()
> refene2.set_pKa(5.03, deprotonated=True)
>
> PTN = TitratableResidue('PTN', ['CB', 'HB2', 'HB3', 'HB4', 'CA', 'CB5', 'HB6', 'HB7', 'HB8', 'CB9', 'HB10', 'HB11', 'HB12', 'C', 'O', 'OZ', 'H'], pka=5.03)
> PTN.add_state(protcnt=1, refene=refene1, # protonated
> charges=[-0.180, 0.600, 0.600, 0.600, 0.000, -0.180, 0.600, 0.600, 0.600, -0.180, 0.600, 0.600, 0.600, 0.520, -0.440, -0.530, 0.450])
> PTN.add_state(protcnt=0, refene=refene2, # deprotonated
> charges=[-0.180, 0.600, 0.600, 0.600, -0.100, -0.180, 0.600, 0.600, 0.600, -0.180, 0.600, 0.600, 0.600, 0.700, -0.800, -0.800, 0.000])
> PTN.check()
> ???????????----------------------------------------------------------------
> I also added this residue under amino acid list in residues.py file & titratable_residues.py (AmberTools/src/parmed/chemistry/amber).
>
> I tried to generate the cpin file for the organic molecule but I run into "residue not titratable" cpin error. I?m not sure what other supplementary files I need to modify to make it work. I would really appreciate your help.
>
> Thanks,
> Arsh
>
> ------------------------------
>
> Message: 5
> Date: Wed, 26 Aug 2015 05:34:47 +0530
> From: anilkumarsahoo.physics.iisc.ernet.in
> Subject: Re: [AMBER] Problem In Performing MMPBSA Calculation for
> System Containing Lipids
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <ec68d77be9042c49d9e02b9a2e8d6eb3.squirrel.physics.iisc.ernet.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi Dan,
>
> I checked the trajectory through the cpptraj 'check' command and found no
> issue. I tried to run with the serial version also, it is giving the same
> error as printed bellow.
>
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA.py", line 104, in ?
> app.parse_output_files()
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/main.py", line 928,
> in parse_output_files
> self.using_chamber)}
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 634, in __init__
> AmberOutput._read(self)
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 343, in _read
> self._get_energies(output_file)
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 661, in _get_energies
> self.data['VDWAALS'].append(float(words[2]))
> ValueError: invalid literal for float(): *************
> Exiting. All files have been retained.
>
> Any help will be really appreciated.
>
> Thanks
> Anil
>
>
>
>> Seems like your coordinates may have some issues. Try running the
>> trajectory through the cpptraj 'check' command to see if you have bad
>> overlaps. Also, you may want to try running a few frames in serial to
>> see if you have similar problems.
>>
>> -Dan
>>
>> On Tue, Aug 25, 2015 at 5:29 AM, <anilkumarsahoo.physics.iisc.ernet.in>
>> wrote:
>>> Dear AMBER users,
>>>
>>> I have installed MMPBSA.py.MPI module of AmberTools14 and am able to
>>> perform binding energy calculation using that. But when I am including
>>> any
>>> Lipid residue in the system, it is giving the following error
>>>
>>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA.py.MPI", line 104, in ?
>>> app.parse_output_files()
>>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/main.py", line 928,
>>> in parse_output_files
>>> self.using_chamber)}
>>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>>> line 634, in __init__
>>> AmberOutput._read(self)
>>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>>> line 343, in _read
>>> self._get_energies(output_file)
>>> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
>>> line 661, in _get_energies
>>> self.data['VDWAALS'].append(float(words[2]))
>>> ValueError: invalid literal for float(): *************
>>> Error occured on rank 0.
>>> Exiting. All files have been retained.
>>>
>>>
>>> My input file for the calculation is given bellow.
>>>
>>> &general
>>> startframe=1, endframe=200, interval=1, keep_files=2, verbose=2,
>>> netcdf=1, use_sander=1,
>>> /
>>> &gb
>>> igb=2, saltcon=0.0,
>>> /
>>>
>>> Thanks for any help,
>>> Anil Kumar Sahoo
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
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>>>
>>>
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>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>>
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>> believed to be clean.
>
>
>
> --
> This message has been scanned for viruses and
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> believed to be clean.
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 25 Aug 2015 22:21:50 -0400
> From: Joseph Baker <bakerj.tcnj.edu>
> Subject: Re: [AMBER] closest command in cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAK3R7NgzSpHKUnY4+wXewWL5qubwTq44y1NtmM1G-_6fKFdrww.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Dan,
>
> Sorry, no warnings or errors. Was just running up against the strip
> commands not seeming to influence things that had been read in using
> loadcrd. For example, the strip :1-4 didn't get rid of those solute
> residues. Also, if I tried to add a strip command after loadcrd like below
> (in just a simple script)
>
> parm test.parm7
> solvent :A
> loadcrd test.nc 1 10 ClosestA
> strip :B
> crdaction ClosestA closest 10 :1-4
> crdout ClosestA Combined.pdb
>
> B does not get stripped from the resulting trajectory written by crdout. So
> basically it was finding the closest A and B, but was not getting rid of
> all of the other A's and B's (which got kept as part of the solute).
>
> The cpptraj version is 15.00
>
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Received on Thu Aug 27 2015 - 09:00:03 PDT
