[gmx-users] new rtp file generation

[David van der Spoel]

안세나 wrote:
> Dear gmx-usr
>  
> I would like to make *.top with the myoglobin pdb file which contain CO 
> ligand like this form.
>  
> HETATM 1268  C   CMO   155      35.753   5.930  11.242  0.77 12.30     
> 1MLF1367
> HETATM 1269  O   CMO   155      35.946   6.791  11.935  0.77 12.70     
> 1MLF1368
>  
> However, this pdb file regards CO ligand as CMO residue, so I  added the 
> information
> for CMO residue to ffG43a1.rtp (I used 0 forcefield.) like this.
>  
> [CMO]
>    [atoms]
>     C     C     0.383  0
>     O     O   -0.383  0
>    [bonds]
>     C     O
> And, I also added CMO residue to aminoacids.dat.
>  
> But, the result of pdb2gmx said "Atom CA cannot found in residue CMO156 
> while adding hydrogen.
>  
> What's the problem?
> Is it right to use rtp file, if not,  should I make *.itp file regarding 
> CO ligand as a molecule?
> Please tell me the answer. Thank you.
give the molecule another chain label. pdb2gmx thinks it is part of the 
polypeptide chain. make sure to use the -ter flag
>  
> Bye, 
> Sena
>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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