[gmx-users] new molecule.itp problem

[David]

On Sat, 2003-06-21 at 13:17, Shavkat Mamatkulov wrote:
> 
> 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.
> 
it's a matter of force field, in OPLS the atomtypes have different name
(opls_XXX, check ffoplsaa.atp) If you want to use this you have to
#include "ffoplsaa.itp"
and modify the topology of your newmolecule.


> 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
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++