[gmx-users] Re: Re: Loss of bonds in HEME iron after pdb2gmx
saradas at ncbs.res.in
saradas at ncbs.res.in
Thu Nov 27 06:06:52 CET 2008
Hi Justin,
Thanks a lot for the suggestions regarding the force field and the
sulphide bond. The bond is now formed after changing the distance range in
specbond.dat.
Thanks.
Sarada
>
> Message: 2
> Date: Wed, 26 Nov 2008 07:21:37 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <492D3F51.4020708 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> saradas at ncbs.res.in wrote:
>> Hi Justin,
>> Thanks for your reply. I am using the gmx Gromacs Forcefield. As you
>> said
>> the topology file does contain the bonds and I need not have made the
>> modificatins to specbond.dat. But using the original specbond.dat does
>> not
>> prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb
>> file and used the following command line
>> pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p
>> topology.top -water spce
>> Am I missing some crucial option here (like -ss for disulphide bonds)?
>> Thanks once again.
>
> One piece of general advice - don't use ffgmx. It has long been
> deprecated
> (according to the manual, the output of pdb2gmx, and dozens of posts on
> this
> list). Use one of the newer Gromos96 force fields.
>
> Now, to address the actual question :) The only thing I can think of is
> that
> specbond.dat uses a simple distance search to determine if the atoms are
> bonded,
> and I believe the tolerance is something like 10%. So the value in
> specbond.dat
> of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25
> +/- 0.2
> nm apart. If they are much further apart, no bond will be detected.
> Check your
> input .pdb file to see how far apart these two atoms are.
>
> -Justin
>
>> Regards,
>> Sarada
>>
>>
>>> Message: 6
>>> Date: Tue, 25 Nov 2008 07:17:14 -0500
>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <492BECCA.5000708 at vt.edu>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>
>>>
>>>
>>> saradas at ncbs.res.in wrote:
>>>> Hello,
>>>> Sorry, I realised the HEME HEC naming was not the problem. But still
>>>> the
>>>> pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
>>>> protonated and doesnot form a bond with HEME. I tried to preserve the
>>>> bonds by editing the specbond.dat file. I do not know if it can be
>>>> used
>>>> for intramolecular bonding. Kindly inform if the modifications I have
>>>> made
>>>> are valid. The runtime information during the execution of pdb2gmx
>>>> indicated the linking of FE in HEME to the N atoms. However, I do not
>>>> see
>>>> the bonds when I open the output file in Pymol. Please indicate how
>>>> this
>>>> problem can be resolved.
>>>>
>>> Well, using visualization software may not indicate anything. Most
>>> programs
>>> decide on bonds based on distance, not any sort of intelligent
>>> mechanism.
>>> The
>>> question is whether or not these bonds show up in your topol.top.
>>>
>>>> This is the content of my specbond.dat file:
>>>>
>>>> 5
>>>> CYS SG 1 HEME FE 5 0.25 CYS HEME
>>> Well, this may be why your Cys is getting protonated - you're telling
>>> pdb2gmx
>>> that it should be! See the format of specbond.dat here:
>>>
>>> http://wiki.gromacs.org/index.php/specbond.dat
>>>
>>> The second-to-last column should be the new residue name for cysteine,
>>> probably
>>> you want something like CYS2.
>>>
>>>> HEME FE 5 HEME NA 3 0.22 HEME HEME
>>>> HEME FE 5 HEME NB 3 0.22 HEME HEME
>>>> HEME FE 5 HEME NC 3 0.22 HEME HEME
>>>> HEME FE 5 HEME ND 3 0.22 HEME HEME
>>>>
>>> Why is this section (above) even necessary? Are these bonds not
>>> defined
>>> in the
>>> .rtp file of your force field? Which force field are you using? I
>>> know
>>> these
>>> are defined in the Gromos-type force fields.
>>>
>>> Try again with the original specbond.dat, but don't assume that
>>> visualization
>>> software will always indicate the presence/absence of a bond. Examine
>>> your
>>> topology for that.
>>>
>>> -Justin
>>>
>>>> And these I obtained during the execution of pdbgmx:
>>>>
>>>> Opening library file specbond.dat
>>>> 5 out of 5 lines of specbond.dat converted succesfully
>>>> Special Atom Distance matrix:
>>>> CYS122 CYS135 CYS143 CYS146 CYS150 CYS237
>>>> CYS309
>>>> SG958 SG1059 SG1118 SG1136 SG1165 SG1902
>>>> SG2475
>>>> CYS135 SG1059 1.677
>>>> CYS143 SG1118 1.076 1.092
>>>> CYS146 SG1136 1.313 1.792 0.749
>>>> CYS150 SG1165 1.175 2.054 0.978 0.426
>>>> CYS237 SG1902 2.194 3.510 2.536 1.933 1.632
>>>> CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449
>>>> CYS343 SG2748 4.679 4.998 4.364 3.763 3.870 3.329
>>>> 4.426
>>>> CYS406 SG3265 2.258 2.657 2.051 1.603 1.744 1.886
>>>> 2.198
>>>> CYS457 SG3657 2.232 0.829 1.894 2.582 2.825 4.173
>>>> 2.898
>>>> HEME462 FE3693 2.257 2.566 1.949 1.489 1.669 1.956
>>>> 2.343
>>>> HEME462 NA3694 2.456 2.680 2.110 1.663 1.862 2.118
>>>> 2.486
>>>> HEME462 NB3695 2.199 2.426 1.883 1.498 1.704 2.088
>>>> 2.247
>>>> HEME462 NC3696 2.061 2.462 1.795 1.321 1.479 1.809
>>>> 2.217
>>>> HEME462 ND3697 2.331 2.711 2.031 1.505 1.657 1.841
>>>> 2.455
>>>> CYS343 CYS406 CYS457 HEME462 HEME462 HEME462
>>>> HEME462
>>>> SG2748 SG3265 SG3657 FE3693 NA3694 NB3695
>>>> NC3696
>>>> CYS406 SG3265 2.501
>>>> CYS457 SG3657 5.547 3.210
>>>> HEME462 FE3693 2.512 0.219 3.147
>>>> HEME462 NA3694 2.361 0.325 3.240 0.211
>>>> HEME462 NB3695 2.647 0.293 2.977 0.208 0.295
>>>> HEME462 NC3696 2.671 0.286 3.064 0.209 0.420 0.297
>>>> HEME462 ND3697 2.389 0.314 3.318 0.208 0.297 0.416
>>>> 0.293
>>>>
>>>>
>>>> Linking HEME-462 FE-3693 and HEME-462 NA-3694...
>>>> Linking HEME-462 FE-3693 and HEME-462 NB-3695...
>>>> Linking HEME-462 FE-3693 and HEME-462 NC-3696...
>>>> Linking HEME-462 FE-3693 and HEME-462 ND-3697...
>>>> N-terminus: PRO-NH2+
>>>> C-terminus: COO-
>>>> Now there are 462 residues with 4749 atoms
>>>> Making bonds...
>>>>
>>>> Thanks.
>>>> Sarada
>>>> Graduate Student,
>>>> NCBS, Bangalore
>>>>
>>>>
>>>>
>>>>
>>>> Hello,
>>>> I am working with the simulation of cytochromeP450. In the output of
>>>> the
>>>> pdb2gmx command, the iron atom in the HEME loses all the bonds,
>>>> including
>>>> the sulphide bond with cystine. Also, the command changed the residue
>>>> name
>>>> from HEME to HEC. During the execution of the pdb2gmx, I get this
>>>> warning:
>>>>
>>>> Warning: 'HEC' not found in residue topology database, trying to use
>>>> 'HEME'
>>>>
>>>> Can someone please tell me, if this is responsible for the loss of
>>>> bonds
>>>> especially the one between CYS and FE. How can the bonds be retained?
>>>> Thanks.
>>>> Sarada
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>>
>>> ------------------------------
>>>
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>>> End of gmx-users Digest, Vol 55, Issue 132
>>> ******************************************
>>>
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 26 Nov 2008 07:25:07 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <492D4023.3060206 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> Justin A. Lemkul wrote:
>
>> S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further
>
> Edit that: 0.25 nm +/- 0.02 nm. Apparently my math (and/or typing) skills
> are
> suspect first thing in the morning :)
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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