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

[saradas at ncbs.res.in]

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.

This is the content of my specbond.dat file:

5
CYS     SG      1       HEME    FE      5       0.25    CYS     HEME
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

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