[gmx-users] new molecule.itp problem

[Shavkat Mamatkulov]

Hi David,

Thanks for your responce

Yes, exactly i am using CH2 atom type and i did

genbox -cp molecule.gro -cs tip4p.gro -p water.top
grompp -f tip4p.mdp -c out.gro -p water.top -o test

but this job is crushing.
the last night i have tried to build my molecule by pdb2gmx: this works!
But the question is why when molecule.itp  built manually (without
pdb2gmx) and when job is started, it do not interact with other molecules?

This problem i met earlier also: when i built buckyball.itp (MD with
buckyball  works fine) and inserted
it into DPPC bilayer, buckyball also did not interact with dppc.

Did anybody met this problem?
Thank you in advance,

best wishes, shavkat



I assume you have done something like
#include "spc.itp"
and added waters to the coordinate file (e.g. using genbox).
Now the question is which atomtype you are using for the C atoms in your
molecule?

Normally I'd say you want CH2

>
> I have create a new molecule something like monoatomic polymer chain
> (without pdb2gmx):
>
>   C-C-C-C-....-C
>
> included my molecule.itp into topology file:
>
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> #include "newmolecule.itp"
>
> and runned job: box containing  two molecule .  It seems to be working.
> But when i have dissolved this
> molecule in water, water doesn't feel this molecule at all and job is
> crushed. In other words the molecule doesn't interact with water
molecules.
>
>   Does it mean a bug in molecule.itp or i have lost something else?
>
> Can anyone suggest me what i have to do.
>
I assume you have done something like
#include "spc.itp"
and added waters to the coordinate file (e.g. using genbox).
Now the question is which atomtype you are using for the C atoms in your
molecule?

Normally I'd say you want CH2

Dr. Shavkat Mamatkulov
Sektion Physik,
LMU Theresienstr. 37, 80333
Muenchen
Tel: 49-89-2180 4596
Fax: 49-89-2180 4517
shavkat at theorie.physik.uni-muenchen.de