[gmx-users] formyl-MET residue : No default Proper Dihe. types

[Nuno R. L. Ferreira]

Hello

My protein has a formyl-MET residue at the N-terminus.  I've constructed
this non-standard residue using PRODRG, and named it FME.  After that, done
the normal stuff : include in the .rtp a new entry and changed the
hydrogenDB.
Since the topology that comes off the prodserver comes in GMX style, done
some modifications on the .top to obtain a gromos like style, based on the
MET information of the respective .rtp file.  The FME entry goes at the end
of this e-mail. A contribution to the gmx world, if there's no error on the
top (any comments are welcomed).

Anyway, here's my question.
After creating the top file for my protein with pdb2gmx (no errors on the
prompt output), I've take a look at the top file. Here's a piece of it:


more b4_vacuum_em.top
;
;       File 'b4_vacuum_em.top' was generated
;       By user: nuno (500)
;       On host: host-1-73.quimica.priv
;       At date: Mon Jul 14 14:02:56 2003
;
;       This is your topology file
;       "I Smell Smoke From a Gun Named Extinction" (Pixies)
;
; Include forcefield parameters
#include "ffG43a1.itp"

[ moleculetype ]
; Name            nrexcl
Protein_X           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB
massB
     1          O      1    FME     OF      1      -0.38    15.9994   ;
qtot -0.38
     2        CH1      1    FME     CF      1       0.38     13.019   ; qtot
0
     3          N      1    FME      N      2      -0.28    14.0067   ;
qtot -0.28
     4          H      1    FME      H      2       0.28      1.008   ; qtot
0
     5        CH1      1    FME     CA      3          0     13.019   ; qtot
0
     6        CH2      1    FME     CB      3          0     14.027   ; qtot
0
     7        CH2      1    FME     CG      3          0     14.027   ; qtot
0
     8          S      1    FME     SD      4          0      32.06   ; qtot
0
     9        CH3      1    FME     CE      4          0     15.035   ; qtot
0
    10          C      1    FME      C      5       0.38     12.011   ; qtot
0.38
    11          O      1    FME      O      5      -0.38    15.9994   ; qtot
0
...
...
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2
c3
      c4            c5
    1     2     3     5     1
    2     3     5    10     1    gd_19
...
...

Don't understand why pdb2gmx sees a dihedral between OF CF N CA, since I
don't have it defined on the rtp FME entry. All the other directives are OK.
Working with this top, grompp says: No default Proper Dihe. types, using
zeroes, which correlates with the missing gd type on dihedrals directive.

How can I resolve this?
This dihedral is not "very important" because it's on a terminal, so maybe I
can just comment that line on the top file, or give a coeherent gd value.

Thank you.
Nuno




_____________________________________
; Topology for FME (formyl-MET)
[ FME ]   ; from prodrg and based on MET
  [ atoms ]
  OF       O  -0.380     0
  CF   CH1   0.380     0 ; united atom f.f.
   N        N  -0.280     1
   H         H   0.280     1
  CA   CH1   0.000     2
  CB   CH2   0.000     2
  CG   CH2   0.000     2
  SD         S   0.000     3
  CE    CH3   0.000     3
   C          C   0.380     4
   O          O  -0.380    4
   [ bonds ]
  OF     CF    gb_4  ; based in C  O
  CF       N    gb_9  ; based in  C  +N
   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    CG    gb_26
  CG    SD    gb_30
  SD    CE    gb_29
  [ angles ]
  ;ai     aj    ak  gromos type
  CF     N      H    ga_31 ; based in -C  N  H
   H      N    CA    ga_17
  CF     N    CA    ga_30 ; based in -C  N  CA
   N    CA      C    ga_12
  CA     C    +N    ga_18
  CA     C      O    ga_29
   O      C    +N    ga_32
  OF   CF      N    ga_32 ; based in  O  C  +N
   N    CA    CB    ga_12
   C    CA    CB    ga_12
  CA    CB    CG    ga_14
  CB    CG    SD    ga_15
  CG    SD    CE    ga_3
  [ impropers ]
  ;  ai    aj    ak    al  gromos type
   N    CF    CA     H    gi_1 ; based in  N  -C  CA  H
   C    CA    +N     O    gi_1
  CA     N     C    CB    gi_2
  [ dihedrals ]
  ; ai    aj    ak    al  gromos type
  CF     N    CA     C     gd_19 ; based in  -C  N  CA  C
   N    CA     C    +N     gd_20
   N    CA    CB    CG    gd_17
  CA    CB    CG    SD    gd_17
  CB    CG    SD    CE    gd_13
#######
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
####