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

[Justin A. Lemkul]

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>> 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>>> 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>>>> 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>>
               <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> | (540)

                      231-9080

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

                         ========================================
                         _______________________________________________
                         gmx-users mailing list    gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
               <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
                      <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>>>
                         <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
               <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>> <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
               <mailto: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/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>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>
                      <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>>
                         <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>
                      <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>>>.

                         Can't post? Read
               http://www.gromacs.org/mailing_lists/users.php



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

                  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

                  ========================================
                  _______________________________________________
                  gmx-users mailing list    gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
               <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
                  <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org> <mailto: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/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>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>
                  <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>
               <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>>.
                  Can't post? Read
        http://www.gromacs.org/mailing_lists/users.php



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

           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

           ========================================
           _______________________________________________
           gmx-users mailing list    gmx-users@gromacs.org
        <mailto:gmx-users@gromacs.org>
           <mailto: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/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>
           <mailto:gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>>.
           Can't post? Read http://www.gromacs.org/mailing_lists/users.php



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

    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

    ========================================
    _______________________________________________
    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/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/mailing_lists/users.php



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

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

========================================
_______________________________________________
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/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/mailing_lists/users.php