[gmx-users] The structure property

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 24 21:23:46 CEST 2008

Chih-Ying Lin wrote:
> Hi
>  From the following tutorial, the protein pdb file is downloaded from 
> the Protein Data Bank. Before running the MD simulation, we have to make 
> sure the structure property. I have some questions about this tutorials.
> http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
> 1. Make sure that there are NO Missing residues, missing atoms-
>    http://www.rcsb.org/pdb/files/1lw9.pdb
>     "Search for the presence of REMARK entries with numbers 465 and/or 
> 470. " => there are no REMARK 465 and REMARK 470  ???

These REMARK lines would correspond to missing atoms or residues.  You should 
always search a .pdb file for such lines; I believe that is the point being made.

> 2. The protonation state and side chain orientation of histidine 
> residues may be problematic. => How could I know if they are 
> problematic? => How to do the protonation process on the system?

It is dependent on the protein, and histidines should be protonated according to 
hydrogen bonding networks, whether or not they are involved in catalysis (and 
how the protonation state might affect the active site!), coordination of metal 
ions, etc.

Gromacs will try to guess the appropriate protonation state.  It is your job to 
thoroughly research your system and determine if any special considerations are 

> 3. From the tutorial => "Note the numbers of ions added, and verify that 
> an excess of 8 chloride ions is added for neutralization. Having 
> replaced a number of water molecules with ions, the system topology in 
> 1LW9.top is not correct anymore. Edit the topology file and decrease the 
> number of solvent molecules. Also add a line specifying the number of 
> NA+ ions and a line specifying the amount of CL-. " 
>  => Would you please explain this more?

What genion does is replace water molecules with ions.  So if 8 Cl- are added, 
then 8 water molecules are removed.  The corrections to the topology are thus 
trivial to implement.  Otherwise, you can pass the -p flag to genion and have it 
make the changes for you.


> Thank you very much
> Lin
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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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