From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Mon Oct 24 2005 - 13:51:13 CDT
Yeap, something is wrong with the bonding of your heme. Create a
representation "not protein" and display it in "licorice". You will se
inmmediatly that something is wrong in the middle.
Marcos
On Mon, 24 Oct 2005, Brian Bennion
wrote:
> The heme residues are not correctly annotated in the psf file. The bonds
> are not correct. It appears that some carbon/notrogen atoms are not
> right, especially around the heme that is residue 301. One of the
> nitrogen atoms has two carbon bonds that straddle the iron atom.
>
> That situtation will never be relaxed with minimization and namd will give
> up.
>
>
>
> On Mon, 24 Oct 2005, Nara Dashdorj wrote:
>
>> Marcos and Brian:
>>
>> I am sending the psf and pdb files that are part of my simulation (the
>> particular chain causing the problem). Topology tiltes the structure
>> around the Fe, which goes away during the minimization, but other than
>> that it looks fine to me. The problematic ones are close to the
>> phorphyrin ring!
>> Please let me know what you think?
>>
>>
>> Thanks, Nara
>>
>>
>> PS: Brain, what is second problem, I did not quite get it?
>>
>>
>>
>> Brian Bennion wrote:
>>
>>> What I am trying to say is that it might be possible that the psf file is
>>> messed up and has some extra bonds in it. I would need to see your psf
>>> file and pdb file in vmd to make sure no weird bonds were imposed.
>>> I can't tell if you are using periodic boundaries in your invacuo test
>>> cases, but I would check that a decimal hasn't been misplaced.
>>>
>>> The two cases above have happened to me before so I keep an eye out for
>>> them.
>>>
>>> Regards
>>> Brian
>>>
>>>
>>>
>>> On Mon, 24 Oct 2005, Nara Dashdorj wrote:
>>>
>>>
>>>
>>>> Brian,
>>>>
>>>> No, there is no bond created that is not suppose to be there, you can
>>>> take a look yourself. The pdb code of the protein is 1VF5, there are for
>>>> instance heavy atoms of three residues ARG83, TYR34, and LYS208 within
>>>> 2.6 Ang from the hemes beside the ones that provide ligands.
>>>> Any ideas solve this problem?
>>>>
>>>> Thanks, Nara
>>>>
>>>>
>>>> Brian Bennion wrote:
>>>>
>>>>
>>>>
>>>>> Hello,
>>>>> It appears that a bond is being created that shouldn't exist naturally.
>>>>> Its possible that a bond has been created between the protein and the heme
>>>>> group that isn't supposed to be there. The the bonds in the psf file for
>>>>> the suspicious atoms.
>>>>>
>>>>> Regards
>>>>> Brian
>>>>>
>>>>>
>>>>> On Sun, 23 Oct 2005, Nara Dashdorj wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Dear NAMD Users:
>>>>>>
>>>>>> I am simulation this integral membrane protein that has several
>>>>>> prosthetic groups. After equilibrating my solvated model, which
>>>>>> encompasses protein in lipid membrane (~220 000 atoms), I wanted to
>>>>>> release my protein, but encountered the problem of steric clashes of atoms.
>>>>>>
>>>>>> I narrowed down my problem by simulating my protein chains separately in
>>>>>> vacuum, which resulted in the conclusion of atoms of heme groups are
>>>>>> clashing with protein subunits. I vissually checked it loading into VMD,
>>>>>> which indicates several residues are really close to the hemes (within
>>>>>> ~2 Angstroms). These are not artifact of topology, it is inherent in the
>>>>>> crystal structure (3.0 Angstrom resolution structure).
>>>>>>
>>>>>> These clashes cause huge VDW energy, and simulation produces the
>>>>>> following log, in which NAMD restarts conjugate gradient algorithm
>>>>>> repeadetly without any success...
>>>>>>
>>>>>> Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.27055e-21 (767)
>>>>>> 1.48231e-21 (767)
>>>>>> Info: Entering startup phase 8 with 42778 kB of memory in use.
>>>>>> Info: Finished startup with 94696 kB of memory in use.
>>>>>> TCL: Minimizing for 1000 steps
>>>>>> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
>>>>>> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
>>>>>> ETITLE: TS BOND ANGLE DIHED
>>>>>> IMPRP ELECT VDW BOUNDARY
>>>>>> MISC KINETIC TOTAL TEMP
>>>>>> TOTAL2 TOTAL3 TEMPAVG PRESSURE
>>>>>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>>>>>
>>>>>> ENERGY: 0 41796.6193 16153.7223 1893.0569
>>>>>> 482.6422 781586.9314 99999999.9999 0.0000
>>>>>> 0.0000 0.0000 99999999.9999 0.0000 99999999.9999
>>>>>> 99999999.9999 0.0000 -99999999.9999 -99999999.9999
>>>>>> 2918023.1080 -99999999.9999 -99999999.9999
>>>>>>
>>>>>> INITIAL STEP: 1e-06
>>>>>> GRADIENT TOLERANCE: nan
>>>>>> BRACKET: 0 0 nan nan nan
>>>>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>>>>> INITIAL STEP: 2.5e-07
>>>>>> GRADIENT TOLERANCE: nan
>>>>>> BRACKET: 0 0 nan nan nan
>>>>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>>>>> INITIAL STEP: 6.25e-08
>>>>>> GRADIENT TOLERANCE: nan
>>>>>> BRACKET: 0 0 nan nan nan
>>>>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>>>>> INITIAL STEP: 1.5625e-08
>>>>>> GRADIENT TOLERANCE: nan
>>>>>> BRACKET: 0 0 nan nan nan
>>>>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>>>>> INITIAL STEP: 3.90625e-09
>>>>>> GRADIENT TOLERANCE: nan
>>>>>> BRACKET: 0 0 nan nan nan
>>>>>> RESTARTING CONJUGATE GRADIENT ALGORITHM
>>>>>> INITIAL STEP: 9.76562e-10
>>>>>>
>>>>>> To resolve this, I played with minimization options such as minBabyStep,
>>>>>> minTinyStep, and maximumMove without any success!
>>>>>>
>>>>>> Any ideas to resolve this problem is truly appreciated!
>>>>>>
>>>>>> --nd
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> ************************************************
>>>>> Brian Bennion, Ph.D.
>>>>> Bioscience Directorate
>>>>> Lawrence Livermore National Laboratory
>>>>> P.O. Box 808, L-448 bennion1_at_llnl.gov
>>>>> 7000 East Avenue phone: (925) 422-5722
>>>>> Livermore, CA 94550 fax: (925) 424-6605
>>>>> ************************************************
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>> ************************************************
>>> Brian Bennion, Ph.D.
>>> Bioscience Directorate
>>> Lawrence Livermore National Laboratory
>>> P.O. Box 808, L-448 bennion1_at_llnl.gov
>>> 7000 East Avenue phone: (925) 422-5722
>>> Livermore, CA 94550 fax: (925) 424-6605
>>> ************************************************
>>>
>>>
>>
>>
>
> ************************************************
> Brian Bennion, Ph.D.
> Bioscience Directorate
> Lawrence Livermore National Laboratory
> P.O. Box 808, L-448 bennion1_at_llnl.gov
> 7000 East Avenue phone: (925) 422-5722
> Livermore, CA 94550 fax: (925) 424-6605
> ************************************************
>
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