From: Nara Dashdorj (dnr_at_physics.purdue.edu)
Date: Mon Oct 24 2005 - 14:51:18 CDT
There are several type of hemes, so I had to came with names depending
on ligand nature. I told you about the iron ligand (in the middle) that
relaxes if I just do short simulation, I do not know why topology does
that, but I did not really pay attention to it, since it goes nicely to
natural position.
Regards to the problme, I am talking about nonbonded VDW, which is
caused by the non-liganded residues within the van der waals distance?
Would patched residue cause the problem?
The heme 301, what is wrong with that?
Nara
Marcos Sotomayor wrote:
>
>
> 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
>> ************************************************
>>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:04 CST