[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

saradas at ncbs.res.in saradas at ncbs.res.in
Wed Nov 26 07:56:05 CET 2008 

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.
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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