[gmx-users] Re Multiple Chains

C Johnson helstreak at hotmail.com
Thu Sep 16 03:21:43 CEST 2010

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.

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....

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