[gmx-users] OPLS-FF

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Mar 24 22:53:58 CET 2008

If I understand correctly, the rebuilt residues do not connect to each  
side of the gap correctly? You state about gaps: "actually it  
shouldn't appear after minimisation.", but it is not necessarily true  
that EM is capable of bringing the residues properly close together. I  
think you mean that "actually you wish it didn't appear after  

I suggest that you focus on generating a better starting structure.  
Try a program called loopy  


--- original message ---

Hi all,
My protein contain some missing residues , so I rebuilt missing residues,
although gap is there between helices, my idea is when do minimisation these
gap should disappear. Later trying to use pdb2gmx with OPLS/aa-L FF for
generating gro file for two systems containing protonated and another one is
unprotonated. For protonation i used command in this way . while
unprotonation didn't mention those aminoacid residues.
pdb2gmx -f protin.pdb -his -asp -glu -o prot_H.gro -p pro_H.top -i pro_H.itp
grompp  -f  .mdp -c  .gro -p  .top  -o  out.tpr
mdrun -v -deffnm out
For both systems EM running fine, but when I opened in VMD, unprotonation
protein helices came close means no gap. But in case of protonation it
doesn't happened still gap is there between helices actually it shouldn't
appear after minimisation.
I tried another FF - ff43a1 result gap is disappearing for both systems.
If use OPLS any options we have to mention or if we want to use OPLS -ff how
to protonate the residues
Any comments will be appreciated
Thanks in advance

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