[gmx-users] using pdb2gmx

[Justin A. Lemkul]

oguz gurbulak wrote:
> 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.
> 
> 

You will not be able to use pdb2gmx to generate a topology unless the relevant 
molecules/residues are defined in your force field's .rtp file.

When posting questions, it is best to include the actual error message instead 
of "it didn't work" or some such equivalent.

You could probably use the PRODRG server to generate a topology for a simple 
molecule like n-dodecane.

If you have a .pdb file from Packmol, it can be used within Gromacs without any 
further modification (.gro is not necessary).  You just need an appropriate 
topology for the system.

-Justin

> Thank you very much for your attention.
> 
> 
> 
> Sincerely
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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