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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 23 11:59:02 CEST 2007

Hi Martinez,

pdb2gmx doesn't do that for you. grompp does. With the specbond.dat
you let pdb2gmx find the bonds and list them in the topology. When
running grompp, it will apply a default bond/angle/dihedral type for
bonds/angles/dihedrals listed, but for which no parameters are given,
based on the [ default_*s ]. You can check whether grompp did a good
job by using the -po option, which should contain the full topology as
it is constructed for and present inside the .tpr file. This means
without any #defines, #includes, etc..., everything filled in
explicitly. Sorry I wasn't clear on this point.



On 4/23/07, martinez <nicolas.martinez at ibs.fr> wrote:
> Thank you for your reply Tsjerk
> I have already edited my spec bond.dat file as follows
> 14
> CYS     SG            1      CYS        SG         1      0.2           CYS2    CYS2
> CYS     SG            1      HEME       FE         2      0.25  CYS2    HEME
> CYS     SG            1      HEME       CAB        1       0.2          CYS2    HEME
> CYS     SG            1      HEME       CAC        1       0.2          CYS2    HEME
> HI2     NE2           1      HEME       FE         1       0.2          HIS1            HEME
> CYS     SG      1       FS4     FE1     1       0.23            CS-             FS4
> CYS     SG      1       FS3     FE1     1       0.23            CS-             FS3
> CYS     SG      1       FS4     FE2     1       0.23            CS-              FS4
> HIS        ND1    1       FS4   FE2     1          0.20  HI2             FS4
> CYS     SG      1       FS3     FE2     1       0.23            CS-             FS3
> CYS     SG      1       FS4     FE3     1       0.23             CS-            FS4
> CYS     SG      1       FS3     FE3     1       0.23            CS-      FS3
> CYS     SG      1       FS4     FE4     1       0.23            CS-      FS4
> CYS     SG      1       FS3     FE4     1       0.23            CS-             FS3
> so that pdb2gmx can make bonds between the different residues.
> I also edited my ff...bon.itp file to specify the bondtypes/angletypes
> but my problem is that  pdb2gmx does not specify the bondtype/angletype
> in the topology file, so I guess I did something wrong when I specified
> the bontypes,etc.. in the ff...bon.itp file. How does pdb2gmx "find"
> the bondtype/angletype for these special bonds in the ff...bon.itp
> file?
> For the histidine ligand, what i had to do is edit the pdb and rename
> the his residue that bonds iron HI2, I couldn't get the histidines in
> the special atom matrix.
> Thanks in advance
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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