[gmx-users] No default Proper Dih. types

[vivek modi]

hi,

I am simulating a protein complex. The peptide in the complex has PRO at the
N-terminal.
I run pdb2gmx and choose PRO-NH as the cap for the respective N-terminal.

pdb2gmx_4mpi -f xyz.pdb -o  -ter -ignh -o conf.gro

Select N-terminus type (start)
 0: PRO-NH2+
 1: PRO-NH
 2: NH3+
 3: None
1
N-terminus: PRO-NH

Then I follow the following steps:

editconf_4mpi -f conf.gro -bt cubic -d 1.5 -c -o out.gro

genbox_4mpi -cp out.gro -cs spc216.gro -o solvated.gro -p topol.top

grompp_4mpi -f xyz.mdp -c solvated.gro -p topol.top -o xyz.tpr

grompp displays the following error:

ERROR 1 [file topol_B.itp, line 1283]:
  No default Proper Dih. types

**following is line 1283 of topol_B.itp:

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    6     1     3     4
1
#THIS IS EMPTY
    3     1     6     5     1    gd_19
    1     3     4     5     1    gd_17
    1     3     7     9     1    gd_20
    3     4     5     6     1    gd_17

Atoms 1-6 come from the terminal PRO and are defined like this in the
topology:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1          N      1    PRO      N      1      -0.28    14.0067   ; qtot
-0.28
     2          H      1    PRO      H      1       0.28      1.008   ; qtot
0
     3        CH1      1    PRO     CA      2          0     13.019   ; qtot
0
     4        CH2      1    PRO     CB      2          0     14.027   ; qtot
0
     5        CH2      1    PRO     CG      3          0     14.027   ; qtot
0
     6        CH2      1    PRO     CD      3          0     14.027   ; qtot
0
     7          C      1    PRO      C      4       0.38     12.011   ; qtot
0.38
     8          O      1    PRO      O      4      -0.38    15.9994   ; qtot
0


Now I do not encounter this problem when I choose PRO-NH2+ as the N-terminal
cap. The diehedral is defined for NH2+ cap.
I am unable to understand that why grompp gives a diehedral error for PRO-NH
and everything is fine if I use PRO-NH2+.

Any help that how can I overcome this problem if I want to use PRO-NH as
N-terminal cap.



Thanks,

Vivek,
Graduate Student,
IITK.
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