[gmx-users] new molecule.itp problem

[David]

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):
> 
>   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



> Thank you in advance
> 
> 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
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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