[gmx-users] PBC - Protein - ligand
s.neumann08 at gmail.com
Mon Nov 7 17:17:31 CET 2011
On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Steven Neumann wrote:
>> Dear Gmx Users,
>> I know that this problem has been discussed may times but I cannot find
>> the solution to get rid of pbc in my system: protein and ligand. I followed
>> the workflow:
>> 1. First make your molecules whole if you want them whole
>> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
>> 2. Cluster your molecules/particles if you want them clustered
>> 3. Extract the first frame from the trajectory as reference for
>> removing jumps if you want to remove jumps.
>> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
>> 4. Remove jumps if you want to have them removed using the first
>> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
>> 5. Center your system using some criterion. Doing so shifts the
>> system, so don't use |trjconv -|pbc| nojump| after this step.
>> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>> 6. Put everything in some box.
>> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o
>> 7. Fit if desired and don't use any PBC related option afterwards.
>> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
>> I used SYSTEM everywhere as output orinput. However, my ligand is still
>> jumping like a fly around the stable protein. Do you have any suggestions?
> Center on either the protein, the ligand, or some custom index group of
> residues surrounding the ligand. Centering on the whole system usually
> doesn't do anything useful.
Thank you guys but...
I am trying and it does not work... my ligand is jumping like an idiot
outside the box changing its position even two dimensions of box in one
frame. I removed -ur compact from the first line and I tried centering on
ligand or protein (centering group: LIG or Protein, output: SYSTEM). No
My ligand at the begining of the simualtion is not within the protein.
Please, help :(((( I tried this workflow with many ligands and same protein
- it worked! Now it does not...
Here is my workflow:
1. First make your molecules whole if you want them whole.
trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc
2. Cluster your molecules/particles if you want them clustered
3. Extract the first frame from the trajectory as reference for
removing jumps if you want to remove jumps.
trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
4. Remove jumps if you want to have them removed using the first frame
trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
5. Center your system using some criterion. Doing so shifts the
system, so don't use trjconv -pbc nojump after this step (tried centering
on LIG or PROTEIN)
trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o
6. Put everything in some box.
trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc
7. Fit if desired and don't use any PBC related option afterwards.
trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
With point three, the issue is that
the jumps from the first frame using the reference structure
provided with -s. If the reference structure (run input file) is not
clustered/whole, trjconv -pbc nojump will undo steps 1 and
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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