[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 03:26:08 CEST 2010

C Johnson wrote:
> """
> Were all of your termini treated correctly here?  If you pass multiple chains to 
> pdb2gmx, the potential problem is that pdb2gmx will read the entire structure as 
> one protein, thus trying to connect sequential N- and C-termini.  This is why 
> the example on the wiki is pertinent - generate a topology for a single 
> polypeptide, then (in your case) change the [molecules] section to reflect the 
> fact that you're building a system with 8 protein molecules (instead of just 1). 
>   Use the pdb2gmx-processed coordinate file as input into genconf and so forth.
> -Justin
> """
> I'm lost :(
> I have a feeling that pdb2gmx is probably converting it to one big protein.

You can turn "probably" into a definitive answer by looking at whether or not 
the termini are protonated properly and if bonds are being assigned between 
sequential N- and C-termini.

> Procedure at this point.
> genconf -f polygly.pdb -nbox 2 2 2 -shuffle  -o did_it_work.pdb
> pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro
> 0: GROMOS96 43a1 force field
> vi polygly.top
> Changed proteins to 8
> At this point I have no clue what to do....

genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro

Have you done any basic tutorial material before diving head-first into this 
more complicated topic?

The idea is this: pdb2gmx generates the topology for the protein.  You can then 
do whatever you choose with this definition of a protein.  After pdb2gmx, you 
also have a coordinate file that meets force field specifications as far as 
protonation goes.  This is the set of coordinates you should replicate, since it 
is correct within the force field.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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