[gmx-users] Protein - Ligand tetramer simulation

Ankita naithani ankitanaithani at gmail.com
Thu Aug 9 17:24:42 CEST 2012

Hi Justin,

Thank you so much for a swift response. I will try as suggested and
get back to you with my hurdles.

Appreciate the help!

Best Wishes,


On Thu, Aug 9, 2012 at 4:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 8/9/12 10:40 AM, Ankita naithani wrote:
>> Hi all,
>> I am trying to put a tetrameric protein for Energy Minimization to be
>> followed by MD simulation of course. But, my problem is that it is a
>> tetramer and also I need to perform the simulation with the ligand. I
>> have read the tutorial for Protein-Ligand simulation but that explains
>> for only one chain, whereas I am talking about 4 chains here.
>> I need to put in my tetramer with ligands attached for simulations.
>> If I have understood correctly, the tutorial mentions about extracting
>> the ligand from PDB and then copying the PDB file of the extracted
>> ligand into PRODRG and then retrieving the topology file from there
>> and appending it to the topology output of the protein without ligands
>> attached. But this is specific for one chain i.e. the PDB co-ordinate
>> given to PRODRG is for the ligand from one chain.
> Yes, and you would have to acquire properly processed coordinates for each
> copy of the ligand.  You only need one .itp file (which in theory should be
> the same, regardless of which copy of the ligand you input to PRODRG), but
> you need coordinate files for the four copies of the ligands from each
> chain.  These would then be appended to the processed protein coordinate
> file in the same manner as the tutorial suggests.
> PRODRG topologies require significant modification to be considered viable
> for real simulation use.  See hints in the tutorial and associated
> publications.
>> The second question is that can I not submit the whole protein-ligand
>> complex to GROMACS and then run pdb2gmx for generating topology. How
>> do I go about that? I understand that I would have to change the top
>> directories of GROMACS to accommodate my ligands but I don't know how
>> to do that.
> Run pdb2gmx on the protein only, then append ligand coordinates as suggested
> above.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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Ankita Naithani

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