Oliver Masur wrote:
<snip>
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.
Works, as in, it correctly places your H2PO4 in the box, or just that the
command runs without error? I don't know about the problem with updating the
topology, but you've got a lot going on at once; maybe that combination breaks
something. You could do everything in two steps to make life easier:
genbox -cp protein.gro -ci h2po4.gro -nmol 1 -p protein.top
genbox -cp out.gro -cs spc216.gro -p protein.top
When i try to grompp then this error occures:
"no such moleculetype h2po4"
That comes up because you either haven't included the right .itp for H2PO4, or
you've included it in the wrong order.
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!
Which .gro file did you have to write? Inserting Na+ or Cl- is the purpose of
genion; were you doing this manually?
-Justin
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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--
========================================
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
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