[gmx-users] new molecule.itp problem
spoel at xray.bmc.uu.se
Fri Jun 20 16:14:01 CEST 2003
On Fri, 2003-06-20 at 16:02, Shavkat Mamatkulov wrote:
> Dear Gromacs users,
> I have create a new molecule something like monoatomic polymer chain
> (without pdb2gmx):
> 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
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
Normally I'd say you want CH2
> Thank you in advance
> Dr. Shavkat Mamatkulov
> Sektion Physik,
> LMU Theresienstr. 37, 80333
> Tel: 49-89-2180 4596
> Fax: 49-89-2180 4517
> shavkat at theorie.physik.uni-muenchen.de
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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