[gmx-users] Re Multiple Chains

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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