[gmx-users] pdb files

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 7 16:28:38 CET 2009

oguz gurbulak wrote:
> Dear All,
> I want to use packmol pdb files that includes one or two different types 
> of molecules. And I seached Gromacs manuals, tutorials and mail archives 
> in order to have enough information about using packmol pdb files in 
> Gromacs. But I couldn't find any information. So Could you please give 
> me the information about this ? How can I use a packmol pdb file for 
> oplsaa and gromacs united-atom force field in generating .gro and .top 
> files for md simulations?

You will not want to create a topology from these files, because pdb2gmx would 
create a huge mess of files to deal with (a different topology for each chain). 
  What you want is to do is to create .itp files for each individual molecule 
type in your system.  This will probably have to be done by hand if you want to 
use OPLS-AA.  Depending on the complexity of your molecule, you may be able to 
use an .rtp entry, but I would suggest processing a single molecule of this type 
with pdb2gmx to create a .top for that molecule (which can be converted to a 
.itp for later use).

Do not use the "Gromacs force field" (ffgmx); it is deprecated and should not be 
used for new simulations.  Use a newer Gromos96 variant.  You can get 
Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that 
the charges and charge groups assigned by PRODRG are often inconsistent and 
unsatisfactory, requiring manual alteration and validation.

1. Create .itp files for each molecule type individually.
2. Construct a .top yourself, which would be as simple as:

#include "ffoplsaa.itp"

#include "molecule_A.itp"
#include "molecule_B.itp"

#include "spc.itp"
#include "ions.itp"

[ system ]
packmol system

[ molecules ]
Molecule_A    N
Molecule_B    N
SOL           N
(then whatever ions you need, if any)


> Sincerely
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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


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