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
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