[gmx-users] Segmentation fault

[David van der Spoel]

On Tue, 2005-09-06 at 11:13 +0100, Naser, Md Abu wrote:
> Hi All,
> 
> I have included a new amino acid- phosphoserine(PSE) in rtp file.
> Although,I  included the amino acid in ffG43a1.hdb and
> 
> pdb2gmx -f xxx.pdb -o xxx.gro -ignh -missing -p xxx.top, gives
> 
> WARNING: atom H is missing in residue PSE 67 in the pdb file
>          You might need to add atom H to the hydrogen database of
> residue PSE
>          in the file ff???.hdb
> 
> When I run mdrun, i am getting segmentation fault.
> 
> 
> Can anyone advise me where might be problem?
You should remove the second H (to OG) from the hdb file, since it is
not there anymore.

> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>  in ffG43a1.rtp
> [ PSE ]
> 
>  [ atoms ]
>     N     N    -0.28000     0
>     H     H     0.28000     0
>    CA   CH1     0.00000     1
>    CB   CH2     0.15000     2
>    OG    OA    -0.54800     2
>    P     P      0.79800     2
>    O1P   OM    -0.80000     2
>    O2P   OM    -0.80000     2
>    O3P   OM    -0.80000     2
>     C     C       0.380     3
>     O     O      -0.380     3
>  [ bonds ]
>     N     H    gb_2   
>     N    CA    gb_20  
>    CA     C    gb_26  
>     C     O    gb_4   
>     C    +N    gb_9   
>    CA    CB    gb_26  
>    CB    OG    gb_17  
>     P    O1P   ga_23
>     P    O2P   ga_23
>     P    O3P   ga_23
>     P    OG    ga_27 
>  [ angles ]
> ;  ai    aj    ak   gromos type
>    -C     N     H     ga_31  
>     H     N    CA     ga_17  
>    -C     N    CA     ga_30  
>     N    CA     C     ga_12  
>    CA     C    +N     ga_18  
>    CA     C     O     ga_29  
>     O     C    +N     ga_32  
>     N    CA    CB     ga_12  
>     C    CA    CB     ga_12  
>    CA    CB    OG     ga_12 
>    OG     P    O1P    ga_23
>    OG     P    O2P    ga_23
>    OG     P    O3P    ga_23
>    CB    OG     P     ga_27
>    O1P    P    O2P    ga_28
>    O1P    P    O3P    ga_28
>    O2P    P    O3P    ga_28
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>     N    -C    CA     H     gi_1   
>     C    CA    +N     O     gi_1   
>    CA     N     C    CB     gi_2   
>  [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>   -CA    -C     N    CA     gd_4   
>    -C     N    CA     C     gd_19  
>     N    CA     C    +N     gd_20  
>     N    CA    CB    OG     gd_17  
>    CA    CB    OG     P     gd_12
>    CB    OG     P   O1P     gd_11
>    CB    OG     P   O2P     gd_11
>    CB    OG     P   O3P     gd_11
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> in ffG43a1.hdb
> PSE     2
>         1       1       N       -C      CA    
>         1       2       OG       CB     CA
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
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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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