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

[Tsjerk Wassenaar]

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.

Best,

Tsjerk

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