Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
Ok. I guess that makes sense. If you say I can send you my system.gro 
file (after catting the system as per our recent conversation) and my 
protein.gro and lipid.gro files (In which the protein is inserted before 
our conversation) and if you visualize that in VMD you will get more 
idea of what I am trying to ask? Can I do that?


I'm sorry, but no, I don't really have time for extra work right now, nor do I 
know anything about the system you're studying.  That's your job to justify the 
position of the system (and adjust it with editconf -translate, if necessary). 
The position should not simply be an aesthetic observation, it should be based 
on any experimental data available.  And like I said, if it is off slightly from 
center, equilibration may help place it correctly.  With CG, you should be able 
to probe long time frames, over which the system may change quite a bit.

-Justin



On Thu, Oct 29, 2009 at 5:46 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    sunny mishra wrote:

        Well yes I guess I am getting the same thing what I expected but
        now I am little confused here and I don't know how to explain
        you this but I will try. Initially I aligned my protein using
        TMDET results and centered that at ORIGIN and then I centered
        the lipid at origin using geom_center script provided in VMD and
        when I visualized that,  the protein was properly inserted in
        the lipid the way MARTINI folks have shown in their website.


    I am unfamiliar with either of these programs, but I can tell you
    that if you center a molecule at the coordinate origin, that
    location (0, 0, 0) corresponds to the corner of the box, by GROMACS
    convention.  This is probably the root of the problem you were
    seeing.  I do not know what the VMD script does.  I would think them
    both unnecessary for GROMACS use (at least in this application),
    since all manipulations can easily be done with editconf.


        After that I followed your tutorial and made the system.gro file
        by catting lipid and protein and its visualization gives me the
        same thing


    You can't be guaranteed that different procedures will lead to
    compatible alignment, as you have undoubtedly discovered :)


        as I was getting earlier. Now after that when I run the
        inflategro script for the system.gro file and scale the lipid by
        the factor of 4,  the protein goes apart from lipid (I dnt know
        why) and after our recent conversation I did the same thing but
        now the protein is shifted little upwards but still it is at the
        center of lipid. Now I don't know whether this factor will
        matter a lot or not? I hope you got my question.


    I don't know how you define "shifted upwards" - relative to where
    editconf placed it, or relative to where you want it to be?  If it
    is not too far from the center, and the proper positioning is to
    have the center of the protein aligned with the center of the
    bilayer, it may assume this position after some equilibration.

    -Justin

        In summary, earlier the upper portion of protein was inserted
        fully same as shown in the martini website but after doing the
        inflategro without running EM it shifted little upwards but
        still at the center so I dnt know whether this will matter a lot
        or not?



        On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           sunny mishra wrote:

               Alright. I have done this....I have made another
               lipid_newbox.gro file and wrote same box vectors as of
        lipid.gro
               file

               For LIPID :

               editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820
               13.29820 6.59160

               For Protein :

               editconf -f protein.gro -o protein_newbox.gro -c -box
        13.29820
               13.29820 6.59160

               Then cat the system and made system.gro file and did
        inflategro
               of the system.gro file. Do you think this is the correct
        way and
               now when I visualize this in VMD the protein is shifted
        little
               upwards but it is at the center of the lipid.


           Well, did you get what you expected when you ran InflateGRO?  The
           protein and lipid should have the same center; that's what the
           editconf commands did, as I've told you.  If you need the
        protein to
           be placed differently, you must specify a different center
           (providing the coordinates to editconf -center).

           -Justin

               Sunny

                           On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul
               <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:



                  sunny mishra wrote:

                      No. But in order to do that with lipid.gro what
        co-ordinates
                      should I have to take?


                  I think you need to differentiate between
        "coordinates" and "box
                  vectors."  You should center the molecule in the box
        (defined
               by the
                  vectors in the last line of the .gro file).  I assumed
        you were
                  specifying these box vectors with -box.

                  So, for both the protein and the lipid coordinate
        files, you
               need to use

                  editconf -c -box (x, y, z from .gro file)

                  -Justin

                      On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
                      <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
                      <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> wrote:



                         sunny mishra wrote:

                             okk...here are the commands which I am givng...

                             editconf -f 1SU4_cleancg_trans.gro -o
               1SU4_newbox.gro -c -box
                             13.29820 13.29820 6.59160

                             I get the 1SU4_newbox.gro which has
        co-ordinates
               13.29820
                             13.29820 6.59160


                         Have you done the same with lipid.gro?  If the
        protein and
                      the lipid
                         are in different coordinate systems (i.e.,
        lipid.gro
               centered
                      at the
                         origin and protein centered within the box,
        which has
               its corner
                         placed at the origin) then you will have a problem.

                         -Justin

                             cat 1SU4_newbox.gro lipid.gro > system..gro

                             Now here system.gro also has co-ordinates
        13.29820
                      13.29820 6.59160

                             now inflategro:

                             inflategro system.gro 4 DSPC 14 -o
               inflated_bilayer.gro 5

                             Now when i visualize my output file in VMD then
               protein and
                             lipid are seperated and even after i scale
        it to
               .95 they dnt
                             meet....they are still apart, I was hoping that
               lipid will be
                             scaled and protein shud have remained in
        the center of
                      the lipid
                             but that doesn't happen. I hope you got my
        question

                             On Thu, Oct 29, 2009 at 4:25 PM, Justin A.
        Lemkul
                             <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
                      <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
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        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>
                             <mailto:jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
                      <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>>> wrote:



                                sunny mishra wrote:

                                    Yes I did the same and when I see my
        system.gro
                      file it
                             gives me
                                    the dimensions of the protein box
        half of
               the lipid
                             bilayer box
                                    so that means it should now be set
        in the
               center
                      of the lipid
                                    bilayer. But after


                                I don't understand what you mean.


                                    that when I run the inflategro
        script and
               see my
                      output
                             file the
                                    protein and lipid are separated and
        I dnt
               know why?


                                Can you post the actual commands you're
        using?

                                -Justin


                                --  
         ========================================

                                Justin A. Lemkul
                                Ph.D. Candidate
                                ICTAS Doctoral Scholar
                                Department of Biochemistry
                                Virginia Tech
                                Blacksburg, VA
                                jalemkul[at]vt.edu <http://vt.edu>
        <http://vt.edu>
               <http://vt.edu> <http://vt.edu>
                      <http://vt.edu> | (540)

                             231-9080

                                     
        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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                         --    ========================================

                         Justin A. Lemkul
                         Ph.D. Candidate
                         ICTAS Doctoral Scholar
                         Department of Biochemistry
                         Virginia Tech
                         Blacksburg, VA
                         jalemkul[at]vt.edu <http://vt.edu>
        <http://vt.edu> <http://vt.edu>
               <http://vt.edu> | (540)
                      231-9080
                       
         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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                  --    ========================================

                  Justin A. Lemkul
                  Ph.D. Candidate
                  ICTAS Doctoral Scholar
                  Department of Biochemistry
                  Virginia Tech
                  Blacksburg, VA
                  jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
        <http://vt.edu> | (540)
               231-9080
                  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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           --    ========================================

           Justin A. Lemkul
           Ph.D. Candidate
           ICTAS Doctoral Scholar
           Department of Biochemistry
           Virginia Tech
           Blacksburg, VA
           jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
        231-9080
           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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    -- 
    ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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