[gmx-users] using pdb2gmx

[oguz gurbulak]

Dear All,



I'm trying to create gro and .top files
using pdb2gmx. I
created  n-dodecane.pdb using Chem3D and  got 100 molecules using
packmol.  I added TER cards between each seperate molecules.  Then I tried to get gro
and .top files using the commands in below :



pdb2gmx
 –ff G43a2
–f 
n-dodecane.pdb  –o n-dodecane.gro –p n-dodecane.top



pdb2gmx
 –ff G43a2
–f 
n-dodecane.packmol100.pdb  –o n-dodecane.gro –p n-dodecane.top (
added TER cards )



pdb2gmx
 –ff G43a2
–f 
n-dodecane.packmol100.pdb  –o n-dodecane.gro –p n-dodecane.top



I
couldn't get  gro and .top files. Could you please help me to get 
gro and .top files successfuly ? I also need some information about
using packmol pdb file in Gromacs. I want to run md for 100 
n-dodecane molecules. 




Thank
you very much for your attention.




Sincerely


      
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