Steven Neumann wrote:
Hi Tsjerk,
Thank you. Unfortunately my ligand is not with protein. I put my ligand
around my protein (in water) running separate simulations to see where
can it bind. It is close to protein but not within. Any other suggestion?
I used also pbc -res so I observe my ligand close to protein but
sometimes still changing its position rapidly... No clue for now how to
solve it...
I have no idea why the proposed protocol isn't working, but I know that one
should be able to do something very simple, along the lines of the following,
for this to work:
1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol
2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the
protein)
3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose protein for
fitting)
-Justin
Steven
On Monday, November 7, 2011, Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>> wrote:
> Hi Steven,
>
> Step 2: Cluster your molecules.
> This is where you have to forge a reference frame that you can use to
> remove jumps from your trajectory. If the ligand is not with the
> protein at the start, you'll have to shift it so that it is. Maybe
> -pbc cluster is your friend there. I do assume that the ligand is
> really with the protein and not in the solvent...
>
> Cheers,
>
> Tsjerk
>
> On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann <s.neuman...@gmail.com
<mailto:s.neuman...@gmail.com>> wrote:
>>
>>
>> On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
>>>> 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.
>>>>
>>>> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
>>>>
>>>> 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
>>>> mdfinal.xtc
>>>>
>>>>
>>>> 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.
>>>
>>> -Justin
>>>
>>
>> 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
>> results...
>> 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
>> (system)
>>
>> 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
>> mdwholeNOjumpCENTER.xtc
>>
>> 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
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
