[gmx-users] new residue en rtp

[David van der Spoel]

On Mon, 2004-06-21 at 02:26, Maximiliano Fra Figueroa Yevenes wrote:
> Hi. I create a new residue in ffgmx.rtp, but the program pdb2gmx send me a
> error:
> Fatal error: Atom HD2 not found in rtp database in residue XXX, it looks a
> bit like H
> 
pdb2gmx -ignh
> My residue is a ASN with a methil group in the N of lateral chain.
> 
> This is the rtp file:
> 
> [ XXX ]
>  [ atoms ]
>      N     N  -0.280     0
>      H     H   0.280     0
>     CA   CH1   0.000     1
>     CB   CH2   0.000     2
>     CG     C   0.380     3
>    OD1     O  -0.380     3
>    ND2     N  -0.280     0
>     HN     H   0.415     4
>     CD   CH3   0.000     1
>      C     C   0.380     5
>      O     O  -0.380     5
>  [ bonds ]
>      N     H
>      N    CA
>     CA     C
>      C     O
>     -C     N
>     CA    CB
>     CB    CG
>     CG   OD1
>     CG   ND2
>    ND2    HN
>    ND2    CD
>  [ impropers ]
>      N    -C    CA     H
>     -C   -CA     N    -O
>     CA     N     C    CB
>     CG   OD1   ND2    CB
>    ND2    HN    CD    CG
> 
> and this the hdb file:
> 
> XXX 	2
> 	1	1	N	-C	CA
> 	1	1	ND2	CG	CB
> 
> Please, I need help. What is wrong?, why I can{t create a topology file or
> why the pdb2gmx ask me for a hudrogen that not exist.
> 
> Thanks
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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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