[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 26 13:21:37 CET 2008
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.
>> 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:
>>> 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
>>> 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
>>> 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
>> decide on bonds based on distance, not any sort of intelligent mechanism.
>> question is whether or not these bonds show up in your topol.top.
>>> This is the content of my specbond.dat file:
>>> CYS SG 1 HEME FE 5 0.25 CYS HEME
>> Well, this may be why your Cys is getting protonated - you're telling
>> that it should be! See the format of specbond.dat here:
>> The second-to-last column should be the new residue name for cysteine,
>> 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
>> are defined in the Gromos-type force fields.
>> Try again with the original specbond.dat, but don't assume that
>> software will always indicate the presence/absence of a bond. Examine
>> topology for that.
>>> 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...
>>> Graduate Student,
>>> NCBS, Bangalore
>>> 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,
>>> the sulphide bond with cystine. Also, the command changed the residue
>>> from HEME to HEC. During the execution of the pdb2gmx, I get this
>>> Warning: 'HEC' not found in residue topology database, trying to use
>>> 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?
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>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list
>> gmx-users at gromacs.org
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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