[gmx-users] Topology for hetroatom (PRODRG)

[David]

On Wed, 2005-02-23 at 22:26 +0530, Alok wrote:
> Hello David,
>                         I include my linker molecule (defined as LIN )in 
> the rtf and hdb files. i also add this LIN in aminoacids.dat file 
> because i want to consider this linker as a part of protein. I also 
> increase the  total count in aminoacids.dat file by one.
>     but pdb2gmx  program does not reconize my linker lolecule (LIN)
> i encounter follwing fatal error..

rtp file.

> 
> Fatal error: Residue 'LIN' not found in residue topology database
> 
> i also check the pdb2gmx.log file (flag -debug) in which it is not 
> reading my linker molecule.
> 
> part of the ouput from the log file generated by pdb2gmx which shows the 
> molecules read by the program from the rtf file is as :
> 
>  80    AR     1          0          0          0          0          0
>  81 SO42-     5          4          6          0          0          0
>  82  ZN2+     1          0          0          0          0          0
>  83   NA+     1          0          0          0          0          0
>  84   CL-     1          0          0          0          0          0
>  85  CA2+     1          0          0          0          0          0
>  86  MG2+     1          0          0          0          0          0
>  87  CU1+     1          0          0          0          0          0
>  88  CU2+     1          0          0          0          0          0
>  89   H2O     3          3          0          0          0          0
>  90   HOH     3          3          0          0          0          0
>  91   HO4     4          3          0          0          0          0
>  92  H2OE     3          3          0          0          0          0
>  93 CHCL3     5          9          0          0          0          0
>  94  DMSO     4          6          0          0          0          0
>  95 CH3OH     3          3          0          0          0          0
>  96  CCL4     5          9          0          0          0          0
>  
> Here in this output i do not find my LIN molecule which is defined after 
> CCL4 in the rtf file.
> 
> Am i going wrong somewhere?? Please suggest.
>                                                                         
>       Thanking you,
>                                                                         
>           Alok Jain
> 
> 
> David wrote:
> 
> >On Wed, 2005-02-23 at 11:52 +0530, Alok wrote:
> >  
> >
> >>hello David,
> >>                   Thank you for your reply.So we will include our 
> >>linker section molecule in the rtf and hdb files.But we are still not 
> >>sure of the parameters we are to take for the linker molecule.Should I 
> >>directly take the parameters mentioned in the ' itp file ' generated by 
> >>the PRODRG server ??????
> >>                          The linker section forms a covalent bond with 
> >>the peptide.The carbonyl group at both ends of the peptide 
> >>(XXX-NH-CH2-CH2-NH-XXX) forms a covalent bond with the amino group at 
> >>the ends of the linker section.
> >>                                           
> >>    
> >>
> >It depends on your force field. 
> >
> >  
> >
> 
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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://xray.bmc.uu.se/~spoel
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