[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.
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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