[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

[Justin A. Lemkul]

Pawan Kumar wrote:
Respected Sir,

Thanks for all your help, suggestions and guidance.
I have few more queries.
Which type of box is appropriate in editconf - cubic or triclinic ?

That depends entirely upon the dimensions of your system and what is adequate to 
accommodate the size of your embedded protein.

I have read in one of your mails in the archives that POPE bilayer 
contains some bad interactions. As it contains more no. of lipids (340) 
it covers the full protein ( trimer which I am working on ) other than 
the few loop regions. How far that bilayer can be used or is it fine to 
use the biger bilayer of popc128a whcih I obtained by genconf ?


The choice of lipid should not be based on a size convenience.  It should be 
based on a valid model system, and experimental evidence to which you can 
correlate your results, if possible.

POPE presented a terrible challenge, since during the in vacuo InflateGRO 
minimizations, the headgroups folded in on themselves to form intra-molecule 
hydrogen bonds that resulted in a collapse of the molecule.  The solution was to 
use freeze-grps in all dimensions during these minimizations, and then 
equilibrate very carefully.

-Justin

Thanking you,
Pawan



On Mon, Mar 23, 2009 at 5:36 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Pawan Kumar wrote:

        Respected Sir,

        Greetings from Pawan.
        Thanks for your reply.
        I used to do genbox first and then Inflategro all the time.
        Is it possible to concatenate one file after the other using "
        vi editor" - I mean just copying the contents of the
        membrane.gro file at the end of protein.gro file ?


    cat protein.gro membrane.gro > system.gro


        Is it fine if I generate the .gro files using editconf command ?


    Yes, you will have to center the protein and membrane appropriately,
    within a box that has the same dimensions.

    -Justin

        Thanks for your kind help.

        Thanking you,
        Pawan

        On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           Pawan Kumar wrote:

               Respected Sir,

               Greetings from Pawan.
               Thanks for your mail.
               I will tell you in detail.
               The control lipid bilayer ( which is generated using genconf
               -nbox 2 2 1 -dist 0 0 0 ) minimized fine with an emtol
        value of
               1510.
               Then after inserting the protein with genbox the whole system
               minimized with an emtol value of 2250.
               Then I am trying to do position restraint mdrun where I am
               getting errors.
               Inflategro can be used only after inserting the protein right
               (which I did using genbox with -vdwd option as 0.6) ?


           No.  Read the documentation carefully.  You first concatenate
        your
           protein and membrane .gro files, then use InflateGRO on that
        system.
            There is no genbox involved when using InflateGRO, hence why I
           suggested it as a (potentially) more reliable method.

           -Justin

               Thanking you,
               Pawan


               On Mon, Mar 23, 2009 at 4:39 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:



                  Pawan Kumar wrote:

                      Hello Justin Sir,

                      Greetings from Pawan.
                      Sorry for the inconvenience.
                      Next time I will keep in mind about the subject line.
                      I tried deleting those particular atoms where it
        gave the
                      maximum force.


                  You said that this atom was part of a lipid.  Deleting
        these
               atoms
                  will give you a broken structure and an unrealistic
        system.  It
                  should also cause grompp to complain.


                      But every time a new atom with a maximum force was
        given
               in the
                      output.
                      Is it fine to use to use "constraints = all-angles" in
               order to
                      overcome the Lincs warnings ?


                  No.  LINCS warnings indicate that there is something
               fundamentally
                  wrong with your system.  It likely stems from how you
               inserted your
                  protein into the lipids.  Think about it.  Your
        control lipid
                  bilayer minimized fine.  Your protein-membrane system does
               not, if
                  that is what we're still talking about. That indicates
        to me that
                  the problem is not with the lipids, the problem is
        with the
                  insertion of the protein.

                  Instead of genbox (which is somewhat crude), try the
        InflateGRO
                  script from Tieleman's site.  I have used it many
        times to build
                  nicely-packed membrane protein systems.  It takes
        substantially
                  longer to build the system than with genbox, but I
        think the
               results
                  are more reliable.

                  -Justin

                      Thanks in advance.

                      Thanking you,
                      Pawan




                      On Mon, Mar 23, 2009 at 4:16 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:


                         When replying to digests, please change the subject
               line to
                         something relevant.

                         Pawan Kumar wrote:

                             Hello Justin Sir,

                             Greetings from Pawan.
                             Sorry for the late reply.
                             The max. force was 1.2447973e+o5 on atom 19448.


                         An Fmax that high is sure to generate problems.
         It is
               up to
                      you to
                         inspect your system, understand which atoms are
               interacting
                      to cause
                         such a force, and determine if you've done
        something
               wrong.

                         -Justin

                             This particular atom belongs to one of the
        lipid
               residues
                      of the
                             bilayer.
                             I get Lincs warnings whenever I run the
        position
                      restraint mdrun.

                             Thanking you,
                             Pawan


                             On Sat, Mar 21, 2009 at 6:08 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>>>>
                             <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:



                                Pawan Kumar wrote:

                                    Hello Justin Sir,

                                    Greetings from Pawan
                                    Thanks for your valuable suggestion
        and reply.
                                    Initially I gave the emtol of 1000
        and the
               output
                      I got was :
                                    Steepest Descents converged to machine
               precision
                      in 163 steps
                                    but did not reach the requested
        Fmax<1000.
                                    Potential Energy = - 4.4516497e+05


                                ...and how close did Fmax get to 1000?


                                    Even I tried to minimize the popc
        bilayer
               which I
                      took from
                                    Tieleman sir's website ( before
        generating a
                      bigger bilayer
                                    using genconf ) but that also
        converged to
               machine
                             precision but
                                    not to the requested Fmax<1000. How do I
               proceed
                      further ?


                                Well, these things are not absolute;
        Fmax = 1000 is
                      kind of a
                             rule
                                of thumb that I use in my own work, but
               sometimes it
                      is not
                                necessary.  Careful equilibration should
               massage your
                      system into
                                cooperating.

                                -Justin

                                    Thanks for your suggestions and help.

                                    Thanking you,
                                    Pawan

                                    On Thu, Mar 19, 2009 at 9:13 PM,

                                       Pawan Kumar wrote:
                                        > Hello Justin Sir,
                                        >
                                        > Greetings from Pawan
                                        > Thanks for your valuable
        suggestion
               and reply.
                                        > After inserting the protein in the
               bilayer using
                             genbox I have
                                       minimized
                                        > the whole system without using any
               position
                      restraints
                                    (i.e. define =
                                        > -DFLEXIBLE in em.mdp file). I used
               vanderwaal's
                             distance
                                    parameter (
                                        > -vdwd of 0.6 ) in the genbox step.
                                        > After running mdrun for energy
               minimization
                      I got the
                                    output as :
                                        > Steepest Descents converged to
               Fmax<2250 in
                      14 steps.
                                        > Potential energy = - 6.9484700e+05
                                        > Maximum force = 2.2114819e+03
        on atom
               34277
                                        > Norm. of force = 5.0103039e+04
                                        >

                                       You should try for an Fmax of no
        greater
               than 1000.
                              2250 is
                                    still
                                       very high.

                                        > I tried decreasing the emtol
        value in
               the em.mdp
                             file but it
                                       ended with
                                        > machine precision.

                                       How far did it converge?  What
        was Fmax?

                                        > I have read in literature that
        5000
               steps of
                      Steetest
                                    Descents run is
                                        > required after inserting the
        protein
               in the
                      bilayer
                             which
                                    should be
                                        > followed by atleast 1000 steps of
               conjugate
                             gradients. How
                                    can I
                                        > accomplish this ? Is there any
               parameter to be
                             given in the
                                       em.mdp file
                                        > ? I use steep as the integrator in
               the mdp
                      file for
                             energy
                                       minimization.

                                       Read the manual.

                                       Whether or not that exact setup
        is going
               to be
                             "required" is
                                    likely
                                       system-specific.  I would say that as
               long as
                      your system
                                    converges
                                       to a stable,
                                       negative Epot with a reasonable Fmax
               (less than
                      1000,
                             but ideally
                                       lower) then
                                       you *may* have an appropriate
        starting
               structure.

                                       -Justin

                                        > Please help with some suggestions.
                                        > Thanks in advance.
                                        >
                                        > Thanking you,
                                        > Pawan
                                        >
                                        >
                                        >



                                                     
        ------------------------------------------------------------------------

                                   
        _______________________________________________
                                    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>>>>
                                    <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
        <mailto:gmx-users@gromacs.org>>>>>

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


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

                                Justin A. Lemkul
                                Graduate Research Assistant
                                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

                                ========================================
                               
        _______________________________________________
                                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>>>>
                                <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
        <mailto:gmx-users@gromacs.org>>>>>

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



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

                         Justin A. Lemkul
                         Graduate Research Assistant
                         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://www.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
                  Graduate Research Assistant
                  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

                  ========================================



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

           Justin A. Lemkul
           Graduate Research Assistant
           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://www.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
    Graduate Research Assistant
    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://www.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
Graduate Research Assistant
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://www.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