»Ø¸´£º Re: [gmx-users] about using amb2gmx.pl

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 16 14:13:19 CET 2008

Quoting xi zhao <zhaoxiitc2002 at yahoo.com.cn>:

> Dear sir :
>   Can you tell me a detail of procedure, I have only chromophore molecular
> top,but I need entire top and gro for pdb + chromophore!

I would invest some serious time in background reading on conducting MD,
especially with Gromacs, as there are plenty of resources available (check out
wiki.gromacs.org, and read as much as you can!)

Of special note, read here:



http://research.ozreef.org/GROMACS_MD_Flowchart.pdf (linked from the above page,
but worth highlighting)

Try out lots of tutorials that do _not_ involve ligands/drugs to get a feel for
the process of conducting some simple MD within Gromacs.  Then search for John
Kerrigan's tutorial for conducting a ligand-enzyme simulation.

Protein structures can be obtained from the RCSB, but as for whether or not a
crystal/NMR structure exists for your protein/chromophore of interest is
anyone's guess.


> Mark Abraham <Mark.Abraham at anu.edu.au> дµÀ£º
>   xi zhao wrote:
> > Dear all users:
> > I want to simulate a system ( protein + chromophore). I
> > have had chromophore.gro and its top file using amb2gmx.pl,but I find I
> > can not use them to translate PDB( protein + chromophore) file into gro
> > and top files properly. So I need your advice about further procedure!
> > Thank you very much
> You don't need a .gro file. See
> http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file
> The grompp utility will happily make a .tpr from your .mdp, your .top
> file, and your well-formed .pdb file whose atom, residue and molecule
> names and ordering matches the .top file. This last constraint also
> applies to a .gro file!
> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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