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 <[EMAIL PROTECTED]> 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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