[gmx-users] Segmentation fault

Naser, Md Abu mn2 at hw.ac.uk
Tue Sep 6 12:13:56 CEST 2005

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?

 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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