[gmx-users] new residue en rtp

Maximiliano Fra Figueroa Yevenes maxfigue at udec.cl
Mon Jun 21 02:26:45 CEST 2004

Hi. I create a new residue in ffgmx.rtp, but the program pdb2gmx send me a
Fatal error: Atom HD2 not found in rtp database in residue XXX, it looks a
bit like H

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.


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