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

[Justin A. Lemkul]

In the manual, have a look at Table 5.4; you are missing lots of parameters 
within the topology (masses, force constants for bonds and angles...)

-Justin

Oliver Masur wrote:
> 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
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================