[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster

[martinez]

Hi gmx users!
I am novice in gromacs and in MD and I've been encountering a couple of 
problems simulating iron sulfur clusters.
The first thing I've done is creating a new residue in the rtp files 
for the 2 clusters.
Then I specified the bonds in the ffG43a1bon.itp file for my sulfur 
iron bonds and modified the specbond.dat file in order to specify the 
cysteine-iron bond and the histidine-iron bond. I also changed the 
ffG43a1.itp file as follows

; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S      S       2    gb_33
NR     FE      2    gb_32
; cystine - heme link (is CR1-S, use CH2-S):
S      CR1     2    gb_30
; cystine - fs link:
FE     S       2    gb_48

[ angletypes ]
CH1    CH2    S     2   ga_15
CH2    S      S     2   ga_5
CR1    NR    FE     2	ga_33
NR     FE    NR     2   ga_16
; cystine - heme link (is CH2-S-CR1, use CH2-S-CH2):
CH2    S     CR1    2   ga_3
; cystine - heme link (is S-CR1-C/CH2, use CHn-CH2-S):
S      CR1   C      2   ga_15
S      CR1   CH2    2   ga_15
; cystine - fs link
S      FE    S      2   ga_47
FE      S    FE     2   ga_48

this is what pdb2gmx tells me
Special Atom Distance matrix:
                    CYS17   CYS20  CYS110  CYS114  CYS147  CYS187  CYS212
                    SG135   SG152   SG812   SG837  SG1062  SG1371  SG1570
    CYS20   SG152   0.651
   CYS110   SG812   1.529   1.023
   CYS114   SG837   0.667   0.660   1.067
   CYS147  SG1062   0.621   0.671   1.411   0.557
   CYS187  SG1371   2.487   2.320   2.869   2.512   2.009
   CYS212  SG1570   2.801   2.726   3.230   2.766   2.278   0.693
   CYS218  SG1617   2.169   2.092   2.625   2.122   1.634   0.648   0.646
   CYS227  SG1685   1.613   1.313   1.896   1.624   1.176   1.044   1.571
   CYS245  SG1828   1.731   1.585   2.100   1.636   1.168   0.926   1.161
   CYS248  SG1846   1.119   0.945   1.592   1.051   0.573   1.464   1.792
   FS4265 FE11986   2.365   2.257   2.769   2.322   1.834   0.478   0.475
   FS4265 FE21988   2.565   2.400   2.838   2.484   2.020   0.464   0.468
   FS4265 FE31990   2.636   2.530   3.034   2.601   2.112   0.490   0.230
   FS4265 FE41992   2.494   2.352   2.875   2.483   1.988   0.229   0.499
   FS4266 FE11994   0.228   0.488   1.329   0.472   0.473   2.406   2.721
   FS4266 FE21996   0.485   0.474   1.119   0.229   0.453   2.418   2.714
   FS4266 FE31998   0.460   0.481   1.283   0.441   0.230   2.179   2.485
   FS4266 FE42000   0.467   0.230   1.126   0.492   0.496   2.318   2.677
   FS3267 FE12002   1.307   1.136   1.778   1.281   0.788   1.236   1.590
   FS3267 FE22004   1.504   1.278   1.901   1.510   1.029   1.044   1.492
   FS3267 FE32006   1.554   1.400   1.991   1.514   1.022   1.000   1.327
                   CYS218  CYS227  CYS245  CYS248  FS4265  FS4265  FS4265
                   SG1617  SG1685  SG1828  SG1846 FE11986 FE21988 FE31990
   CYS227  SG1685   1.037
   CYS245  SG1828   0.530   0.650
   CYS248  SG1846   1.151   0.640   0.648
   FS4265 FE11986   0.230   1.111   0.696   1.326
   FS4265 FE21988   0.481   1.200   0.853   1.487   0.278
   FS4265 FE31990   0.491   1.348   0.975   1.604   0.280   0.273
   FS4265 FE41992   0.480   1.118   0.857   1.454   0.273   0.270   0.277
   FS4266 FE11994   2.080   1.501   1.614   0.985   2.275   2.460   2.550
   FS4266 FE21996   2.068   1.501   1.580   0.958   2.263   2.431   2.542
   FS4266 FE31998   1.840   1.284   1.362   0.734   2.034   2.212   2.312
   FS4266 FE42000   2.036   1.355   1.540   0.893   2.216   2.378   2.492
   FS3267 FE12002   0.960   0.473   0.471   0.230   1.121   1.283   1.396
   FS3267 FE22004   0.906   0.230   0.477   0.473   1.022   1.154   1.281
   FS3267 FE32006   0.701   0.483   0.230   0.477   0.857   1.021   1.132
                   FS4265  FS4266  FS4266  FS4266  FS4266  FS3267  FS3267
                  FE41992 FE11994 FE21996 FE31998 FE42000 FE12002 FE22004
   FS4266 FE11994   2.408
   FS4266 FE21996   2.408   0.266
   FS4266 FE31998   2.173   0.269   0.265
   FS4266 FE42000   2.333   0.272   0.275   0.277
   FS3267 FE12002   1.233   1.192   1.183   0.950   1.101
   FS3267 FE22004   1.080   1.395   1.397   1.167   1.281   0.267
   FS3267 FE32006   0.977   1.444   1.431   1.201   1.364   0.265   0.273


Linking CYS-17 SG-135 and FS4-266 FE1-1994...
Linking CYS-20 SG-152 and FS4-266 FE4-2000...
Linking CYS-114 SG-837 and FS4-266 FE2-1996...
Linking CYS-147 SG-1062 and FS4-266 FE3-1998...
Linking CYS-187 SG-1371 and FS4-265 FE4-1992...
Linking CYS-212 SG-1570 and FS4-265 FE3-1990...
Linking CYS-218 SG-1617 and FS4-265 FE1-1986...
Linking CYS-227 SG-1685 and FS3-267 FE2-2004...
Linking CYS-245 SG-1828 and FS3-267 FE3-2006...
Linking CYS-248 SG-1846 and FS3-267 FE1-2002...
N-terminus: NH3+

I have 2 questions:
Why aren't the histidines in the matrix? I think that the program 
protonates first the histidines before generating the matrix with the 
distances, but I'm not sure...

When I take a look at my topology file, in the[ bonds ] section, this 
is what I see

  2016  2017     2    gb_30
  2017  2490     2
  2018  2019     2    gb_4

where atom 2490 is an iron and atom 2017 is a sulfur atom from a 
cysteine. Why doesn't pdb2gmx specify the bond type? It's really 
strange because pdb2gmx does not give me a message error or a warning 
of any kind.

Thank you for your help.

Nicolas