[gmx-users] C-terminal amide capping

Fri Feb 20 15:28:55 CET 2009

Hi Anita:
you can create the topology of your last residue with CONH2
an example is a LYS-CONH2 I name this residue as LYN, you must include
this residue in aminoacids.dat, ffXXXX.rtp
 [LYN] 
  [ atoms ]
    N     N    -0.31000     0
    H     H     0.31000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     2
   CD   CH2     0.00000     2
   CE   CH2     0.12700     3
   NZ    NL     0.12900     3
  HZ1     H     0.24800     3
  HZ2     H     0.24800     3
  HZ3     H     0.24800     3
    C     C     0.29000     4
    O     O    -0.450       4
  ND2    NT    -0.72000     4
 HD21     H     0.44000     4
 HD22     H     0.44000     4
 [ bonds ]
    N     H    gb_2    
    N    CA    gb_21   
   CA    CB    gb_27   
   CA     C    gb_27   
   CB    CG    gb_27   
   CG    CD    gb_27   
   CD    CE    gb_27   
   CE    NZ    gb_21   
   NZ   HZ1    gb_2    
   NZ   HZ2    gb_2    
   NZ   HZ3    gb_2    
    C     O    gb_5    
    C    ND2   gb_9
  ND2    HD21  gb_2
  ND2    HD22  gb_2
    C    +N    gb_10  
  [ angles ] 
  ;  ai    aj    ak   gromos type
   -C     N     H     ga_32   
   -C     N    CA     ga_31   
    H     N    CA     ga_18   
    N    CA    CB     ga_13   
    N    CA     C     ga_13   
   CB    CA     C     ga_13   
   CA    CB    CG     ga_15   
   CB    CG    CD     ga_15   
   CG    CD    CE     ga_15   
   CD    CE    NZ     ga_15   
   CE    NZ   HZ1     ga_11   
   CE    NZ   HZ2     ga_11   
   CE    NZ   HZ3     ga_11   
  HZ1    NZ   HZ2     ga_10   
  HZ1    NZ   HZ3     ga_10   
  HZ2    NZ   HZ3     ga_10   
   CA     C     O     ga_30      
   CA     C   ND2     ga_19
    O     C   ND2     ga_33
    C   ND2   HD21    ga_23
    C   ND2   HD22    ga_23
  HD21  ND2   HD22    ga_24       
   CA     C    +N     ga_19   
    O     C    +N     ga_33
    [ impropers ] 
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1    
   CA     N     C    CB     gi_2
    C    CA    O    ND2     gi_1
   ND2    C   HD21  HD22    gi_1
    C    CA    +N     O     gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_14   
   -C     N    CA     C     gd_39   
    N    CA    CB    CG     gd_34   
    N    CA     C    +N     gd_40   
   CA    CB    CG    CD     gd_34   
   CB    CG    CD    CE     gd_34   
   CG    CD    CE    NZ     gd_34   
   CD    CE    NZ   HZ1     gd_29
   CB    CA     C   ND2     gd_40
   CA    C    ND2   HD21    gd_14

you must include this ffXXXX.hdb
LYN     3     
1	1	H	N	-C	CA
3	4	HZ	NZ	CE	CD
2	3	HD2	ND2	CG	CB
you must run pdb2gmx as:
pdb2gmx_402 -f test.pdb -o peptidop1_30.gro -p peptidop1_30.top -ff XXXX
-ignh  -i  peptidop1_30_posre.itp -ter 
you must set 
0 for the n-terminal and 2 for the c-terminal

On Fri, 2009-02-20 at 19:15 +0530, ANINDITA GAYEN wrote:
> 
> Dear all,
>             I do simulate DMPC+peptide+water+ions system, using
> OPLS-AA force field.
> My peptide has N-terminus: NH3+ & C-terminus: COO- groups. I want to
> convert it to 
> N-terminus: NH2, C-terminus: CONH2. The N-terminal capping is easily
> done using "pdb2gmx -ter " command, but C-terminal amide capping
> option is not incorporated.
> Can anyone please suggests me how i can achive this?
> Thanks in advance.
> 
> Ms. Anindita Gayen> C/O Dr. Chaitali Mukhopadhyay
> Senior Research Fellow
> Department of Chemistry
> University of Calcutta
> 92, A. P. C. Road
> Kolkata-700 009
> India
> 
> 
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