From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 24 2013 - 15:07:54 CDT
I forgot the forum. Sorry
fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Apr 24, 2013 at 8:07 AM
Subject: Re: vmd-l: HEME acting unplanar
To: Paweł Kędzierski <pawel.kedzierski_at_pwr.wroc.pl>
Unless I missed part of the discussion, I would suggest checking either the
log file from the command to build psf.pdb (vmd -dispdev..?) or the psf
file itself (bonds.. etc) for possible errors in patching. One can get
seemingly workable psf/pdb, though in error as to the patching. Correct
plans as to patching may be overridden by errors in atom ID, or else, which
may led to a fake psf.
Should this be a duplicate suggestion, I beg pardon
francesco pietra
On Tue, Apr 23, 2013 at 10:13 AM, Paweł Kędzierski <
pawel.kedzierski_at_pwr.wroc.pl> wrote:
>
> I am not familiar with heme modeling but this may be a useful hint.
> Angle and dihedral parameters are not in general sufficient to enforce
> planarity. For this purpose one needs "out-of-plane" harmonic force
> constants. These are called "improper dihedrals" in charmm forcefield or
> simply impropers, as the independent variable is a dihedral angle defined
> by four atoms, but the energy term is harmonic instead of periodic.
> It seem possible to me that at creation of your own heme topology file you
> may have omitted the definition of these planarity enforcing parameters.
> Please consult the online charmm documentation, e.g.
> http://www.charmm.org/**documentation/c36b1/rtop.html
> but in short you must provide IMPR lines in the residue topology definition
> (four atom names defining the dihedral, central atom first), and of course
> the relevant parameters must be present in the IMPROPER section of the
> parameter file. I am sure these parameters are available for heme so it may
> only be an omission in the residue topology definition.
> HTH,
> Pawel
>
> W dniu 22.04.2013 21:10, Yarrow Madrona pisze:
>
> Hi Axel,
>>
>> Thank you for your help. I have been learning MD for only a month now so
>> please bare with me. I apologize in advance for this long winded post.
>> Unfortunately, I do not know anyone who has done extensive simulations
>> with cysteine HEME linkage using CHARM parameters. The few I see on line
>> look similar to what I have done but I have no way of knowing whether they
>> see flex in the heme or not.
>>
>> 1. To answer your first question: The first simulations were done with the
>> top_par_22_heme.str streaming file that is input into NAMD. I had the same
>> problems with some non-planarity. kind of looks like a v with the iron at
>> the apex (about 150 to 160 deg). There was also a distance contrain
>> between the cysteine and iron.
>>
>> I have heard in a forum that for a pentacoordinate heme like Myoglobin
>> with Histine coordinating it is better to use the PHEM; His bound to Fe
>> patch in the heme streaming file. It was mentioned that the "The FHEM
>> patch is needed to remove a couple N-Fe-N ANGLE terms added by
>> (AUTO)GENERATE". See
>> http://www.charmm.org/**ubbthreads/ubbthreads.php?ubb=**
>> showflat&Number=25711<http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=25711>
>>
>> I was having a little difficulty understanding how to implement the
>> patches so I built the parmameter file/topology file for a HEME + Cystene
>> residue I called HEC. I defined bonds, Improppers and internal
>> coordinates in the topology file. Most of these come straight from the
>> HEME streaming file with corrections for the new cysteine bond. I also
>> entered the spring constant, distance and angle in the parameter file.
>> Everything behaves well except for that that flexing of the Heme.
>>
>> The only thing that is not in there from the heme streaming file is the
>> following:
>>
>> DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
>> ANGLE 1C1 1S 2FE 1C1 1S 2FE
>> ANGLE 1S 2FE 2NA 1S 2FE 2NB 1S 2FE 2NC 1S 2FE 2ND
>> IC 1C1 1S 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
>> IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
>> IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
>> IC 1C1 1S 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
>>
>> I added the IC's to the parameter file but it does not seem to make a
>> difference. I suppose I can add the delete comment into the psfgen before
>> running it. Should I manually put in the length, dihedral and angle of
>> all of the above?
>>
> The IC lines are only used by psfgen if some atoms are missing in PDB
> coordinates; internal coordinates are then necessary to generate their
> positions relative to present ones. These lines are not used for
> parametrization so most likely you don't need them at all.
>
>
>
>> I already have defined may of them in addition to the ones taken from Heme
>> streaming file:
>>
>> IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
>> IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
>> IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
>> IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
>> IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
>> IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
>> IC N C *CA HAY 1.4533 105.8900 -116.3400 107.7100 1.0837
>> IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
>> IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
>> IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
>> IC CA CB SG FE 1.5584 113.8700 180.0000 111.5140 2.2000
>>
>> Thank you.
>> -Yarrow
>>
>>
>>
>>
>> two comments:
>>> 1) have you made some test calculations with the regular heme residue as
>>>
>> provided in the parameter set to have a reference to compare to? 2)
>> parts of molecules are usually held flat through improper
>>
>>> dihedrals. have you checked whether they are exist where needed and have
>>>
>> assigned parameters for your custom residue? again, it can be extremely
>> helpful to compare to "vanilla" reference.
>>
>>> axel.
>>> On Mon, Apr 22, 2013 at 12:49 AM, Yarrow Madrona <amadrona_at_uci.edu>
>>>
>> wrote:
>>
>>> Hello,
>>>> I know this is a CHARMM question but I am having trouble finding
>>>>
>>> information on this.
>>
>>> I am wondering if anyone here has experience with HEME-cystiene Fe
>>>>
>>> thiol
>>
>>> or Fe-HIS simulation. I recently build a parameter and top file with a
>>>> new
>>>> residue "HEC" which is a combination of the HEME and cysteine as a
>>>> single
>>>> residue. I took most of the HEME parameters from the CHARMM Heme
>>>> streaming
>>>> toppar file.
>>>> Everything looks fine except the HEME seems to flex a little. Looks a
>>>>
>>> little like a "V" Maybe 140-160 deg instead of 180 degrees across the
>> heme. I have heard that there are some parameters to take from the PRES
>> SUL patch in the HEME topar streaming file. I have taken and modified
>> the
>>
>>> relevant ones but I was wondering if anyone knows specifically, what
>>>> would
>>>> cause the heme to be less than ideal planar.
>>>> Thank you for your help.
>>>> --
>>>> Yarrow Madrona
>>>> Graduate Student
>>>> Molecular Biology and Biochemistry Dept.
>>>> University of California, Irvine
>>>> Natural Sciences I, Rm 2403
>>>> Irvine, CA 92697
>>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>>
>
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