[gmx-users] grompp error: Incorrect number of parameters - found 1, expected 2 or 4

[Oliver Masur]

Hi,
i'm still trying to use the genbox command to put h2po4 (aka DHP) in the 
box.

i've got a gro file for h2po4:*
*DHP
   7
    1DHP   O1     1   2.725   1.500   1.066 -0.0608  0.4317 -0.3840
    1DHP   O2     2   0.438   0.887   1.066 -0.1943 -0.6301 -0.3887
    1DHP   O3     3   0.438   2.113   1.066 -0.8067 -0.2363  0.3290
    1DHP   O4     4   1.500   1.500   2.800 -0.8067 -0.2363  0.3290
    1DHP    P     5   1.500   1.500   1.500 -0.2435  0.1688 -0.2164
    1DHP   H1     6  -0.362   2.113   1.066 -0.8067 -0.2363  0.3290
    1DHP   H2     7   3.525   1.500   1.066 -0.8067 -0.2363  0.3290
    2  2  2

i wrote an entry in the rtp file of the forcefield i want to use:
[ DHP ]
 [ atoms ]
    O1     OM  -0.75500    14
    O2     OM  -0.75500    14
    O3     OA  -0.54800    14
    O4     OA  -0.54800    14
     P      P   0.63000    14
    H1      H   0.18300    14
    H2      H   0.18300    14
 [ bonds ]
    P     O3       gb_27
    P     O1       gb_23
    P     O2       gb_23
    P     O4       gb_23
    O3    H1       gb_1
    O4    H2       gb_1
 [ angles ]
   O1     P   O2     ga_4
   O1     P   O3     ga_13
   O1     P   O4     ga_4
   O2     P   O3     ga_13
   O2     P   O4     ga_4
   O3     P   O4     ga_13
   P     O3   H1     ga_11
   P     O4   H2     ga_11
 [ dihedrals ]
   O1    P    O3    H1     gd_11
   O1    P    O3    H1     gd_9
   O1    P    O4    H2     gd_11
   O1    P    O4    H2     gd_9


and the itp file for DHP looks like this:

[ moleculetype ]
DHP     4

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
; use charges from Janez Mavri
     1      OM       1     PI       O1       1          -0.777
     2      OM       1     PI       O2       1          -0.777
     3      OA       1     PI       O3       1          -0.943
     4      OA       1     PI       O4       1          -0.943
     5       P       1     PI        P       1           1.596
     6      H       1     PI       H1       1           0.422
     7      H       1     PI       H2       1           0.422

[ bonds ]
;  ai    aj funct           c0           c1
    5     1     1 1.637000e-01
    5     2     1 1.637000e-01
    5     3     1 1.478000e-01
    5     4     1 1.478000e-01
    6     1     1 0.943000e-01
    7     2     1 0.943000e-01

[ angles ]
;  ai    aj    ak funct           c0     c1
    2     5     1     1 1.015000e+02    400
    3     5     1     1 1.059000e+02
    4     5     1     1 1.082000e+02
    3     5     2     1 1.059000e+02
    4     5     2     1 1.082000e+02
    4     5     3     1 1.248000e+02
    6     1     5     1 1.082000e+02
    7     2     5     1 1.082000e+02

[ dihedrals ]
;  ai    aj    ak    al funct
    6     1     5     2     1
    7     2     5     1     1


i also wrote in the protein.top file after the pdb2gmx command the 
line:  #inlcude "h2po4.itp"  after the "inlcude ions.itp" line.

So i proceed as follows:

pdb2gmx -f protein.pdb -o protein.gro -p protein.top
grompp -f minim.mdp -c protein.gro -p protein.top -o input.tpr
mdrun -s input.tpr -deffnm minid_protein
editconf -f minid_protein.gro -o minid_box.gro -box 10 10 10 -bt cubic
genbox -cp minid_box.gro -cs spc216.gro -ci h2po4.gro -nmol 1 -shell 1 
-p protein.top -o dhp_box.gro
genbox -cp dhp_box.gro -cs spc216.gro -ci na+.gro -nmol 1 -shell 1 -p 
protein.top -o nadhp_box.gro
genbox -cp nadhp_box.gro -cs spc216.gro -protein.top -o nadhp_wat.gro
grompp -f minim.mdp -c nadhp_wat.gro -p protein.top  -o  inputdhp.tpr

with the last command the following error occurs:

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1180

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4.
-------------------------------------------------------

i hope you can help me.
thanks upfront,
   Oliver