[gmx-users] putting extra molecules in the box with genbox

[Oliver Masur]

hello,
i'm trying to put H2PO4 in my box with the genbox command.
I wrote the .gro file myself, or is there a site to download them?
The file looks like this: (the blanks got a little mixed up by copying)

h2po4
   7
    1h2po4   OA     1   2.725   1.500   1.066 -0.0608  0.4317 -0.3840
    1h2po4   OA     2   0.438   0.887   1.066 -0.1943 -0.6301 -0.3887
    1h2po4   OM     3   0.438   2.113   1.066 -0.8067 -0.2363  0.3290
    1h2po4   OM     4   1.500   1.500   2.800 -0.8067 -0.2363  0.3290
    1h2po4       P     5   1.500   1.500   1.500 -0.2435  0.1688 -0.2164
    1h1po4       H     6  -0.362   2.113   1.066 -0.8067 -0.2363  0.3290
    1h2po4       H     7   3.525   1.500   1.066 -0.8067 -0.2363  0.3290
    1  1  1




The .itp file came with gromacs, so i took it:

[ moleculetype ]
; name  nrexcl
h2po4   4

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
; use charges from Janez Mavri
     1      OA       1     PI       O1       1          -0.777
     2      OA       1     PI       O2       1          -0.777
     3      OM       1     PI       O3       1          -0.943
     4      OM       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

I also wrote an entry in the forcefield file i want to use (ffG43a1.rtp) 
for the h2po4 molecule. Unfortunately Gromacs got reinstalled
before i wrote this mail, so the exact entry is unavailable. But i 
orientated myself by the other entries, and i gave it the same name as 
in the gro file.
Probably the mistake was in there, or maybe i've forgot something else.

So i built up my box, then put h2po4 in (and then a counterione) by using
"genbox -cp protein.gro -cs spc216.gro -ci h2po4.gro -nmol 1 -shell 1 
-seed int -o out.gro -p protein.top"

this part works, except that genbox doesn't update protein.top for 
anything else than the water solvens, and i had to put in the h2po4 
group myself.

When i try to grompp then this error occures:
"no such moleculetype h2po4"

And before that, i probably mixed up some atom names because i.e. "no 
such atomtype HO" occured.

The whole thing works for normal ions like Na+ or Cl- where i just had 
to write the gro file!

If someone sees my mistake, or maybe can tell me how extra molecules 
really can be put in the box, i'd immensely appreciate it.
thank you up-front,
Oliver