Respected Sir,<br><br>Greetings from Pawan.<br>Thanks for your reply.<br>I used to do genbox first and then Inflategro all the time.<br>Is it possible to concatenate one file after the other using &quot; vi editor&quot; - I mean just copying the contents of the membrane.gro file at the end of protein.gro file ?<br>
Is it fine if I generate the .gro files using editconf command ?<br>Thanks for your kind help.<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
Thanks for your mail.<br>
I will tell you in detail.<br>
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.<br>
Then after inserting the protein with genbox the whole system minimized with an emtol value of 2250.<br>
Then I am trying to do position restraint mdrun where I am getting errors.<br>
Inflategro can be used only after inserting the protein right (which I did using genbox with -vdwd option as 0.6) ?<br>
<br>
</blockquote>
<br></div>
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.<br>

<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanking you,<br>
Pawan<div class="im"><br>
<br>
On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>

<br>
<br>
<br>
    Pawan Kumar wrote:<br>
<br>
        Hello Justin Sir,<br>
<br></div><div><div></div><div class="h5">
        Greetings from Pawan.<br>
        Sorry for the inconvenience.<br>
        Next time I will keep in mind about the subject line.<br>
        I tried deleting those particular atoms where it gave the<br>
        maximum force.<br>
<br>
<br>
    You said that this atom was part of a lipid.  Deleting these atoms<br>
    will give you a broken structure and an unrealistic system.  It<br>
    should also cause grompp to complain.<br>
<br>
<br>
        But every time a new atom with a maximum force was given in the<br>
        output.<br>
        Is it fine to use to use &quot;constraints = all-angles&quot; in order to<br>
        overcome the Lincs warnings ?<br>
<br>
<br>
    No.  LINCS warnings indicate that there is something fundamentally<br>
    wrong with your system.  It likely stems from how you inserted your<br>
    protein into the lipids.  Think about it.  Your control lipid<br>
    bilayer minimized fine.  Your protein-membrane system does not, if<br>
    that is what we&#39;re still talking about. That indicates to me that<br>
    the problem is not with the lipids, the problem is with the<br>
    insertion of the protein.<br>
<br>
    Instead of genbox (which is somewhat crude), try the InflateGRO<br>
    script from Tieleman&#39;s site.  I have used it many times to build<br>
    nicely-packed membrane protein systems.  It takes substantially<br>
    longer to build the system than with genbox, but I think the results<br>
    are more reliable.<br>
<br>
    -Justin<br>
<br>
        Thanks in advance.<br>
<br>
        Thanking you,<br>
        Pawan<br>
<br>
<br>
<br>
<br>
        On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div></div><div><div></div><div class="h5">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
           When replying to digests, please change the subject line to<br>
           something relevant.<br>
<br>
           Pawan Kumar wrote:<br>
<br>
               Hello Justin Sir,<br>
<br>
               Greetings from Pawan.<br>
               Sorry for the late reply.<br>
               The max. force was 1.2447973e+o5 on atom 19448.<br>
<br>
<br>
           An Fmax that high is sure to generate problems.  It is up to<br>
        you to<br>
           inspect your system, understand which atoms are interacting<br>
        to cause<br>
           such a force, and determine if you&#39;ve done something wrong.<br>
<br>
           -Justin<br>
<br>
               This particular atom belongs to one of the lipid residues<br>
        of the<br>
               bilayer.<br>
               I get Lincs warnings whenever I run the position<br>
        restraint mdrun.<br>
<br>
               Thanking you,<br>
               Pawan<br>
<br>
<br>
               On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul<br>
               &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
                  Pawan Kumar wrote:<br>
<br>
                      Hello Justin Sir,<br>
<br>
                      Greetings from Pawan<br>
                      Thanks for your valuable suggestion and reply.<br>
                      Initially I gave the emtol of 1000 and the output<br>
        I got was :<br>
                      Steepest Descents converged to machine precision<br>
        in 163 steps<br>
                      but did not reach the requested Fmax&lt;1000.<br>
                      Potential Energy = - 4.4516497e+05<br>
<br>
<br>
                  ...and how close did Fmax get to 1000?<br>
<br>
<br>
                      Even I tried to minimize the popc bilayer which I<br>
        took from<br>
                      Tieleman sir&#39;s website ( before generating a<br>
        bigger bilayer<br>
                      using genconf ) but that also converged to machine<br>
               precision but<br>
                      not to the requested Fmax&lt;1000. How do I proceed<br>
        further ?<br>
<br>
<br>
                  Well, these things are not absolute; Fmax = 1000 is<br>
        kind of a<br>
               rule<br>
                  of thumb that I use in my own work, but sometimes it<br>
        is not<br>
                  necessary.  Careful equilibration should massage your<br>
        system into<br>
                  cooperating.<br>
<br>
                  -Justin<br>
<br>
                      Thanks for your suggestions and help.<br>
<br>
                      Thanking you,<br>
                      Pawan<br>
<br>
                      On Thu, Mar 19, 2009 at 9:13 PM,<br>
<br>
                         Pawan Kumar wrote:<br>
                          &gt; Hello Justin Sir,<br>
                          &gt;<br>
                          &gt; Greetings from Pawan<br>
                          &gt; Thanks for your valuable suggestion and reply.<br>
                          &gt; After inserting the protein in the bilayer using<br>
               genbox I have<br>
                         minimized<br>
                          &gt; the whole system without using any position<br>
        restraints<br>
                      (i.e. define =<br>
                          &gt; -DFLEXIBLE in em.mdp file). I used vanderwaal&#39;s<br>
               distance<br>
                      parameter (<br>
                          &gt; -vdwd of 0.6 ) in the genbox step.<br>
                          &gt; After running mdrun for energy minimization<br>
        I got the<br>
                      output as :<br>
                          &gt; Steepest Descents converged to Fmax&lt;2250 in<br>
        14 steps.<br>
                          &gt; Potential energy = - 6.9484700e+05<br>
                          &gt; Maximum force = 2.2114819e+03 on atom 34277<br>
                          &gt; Norm. of force = 5.0103039e+04<br>
                          &gt;<br>
<br>
                         You should try for an Fmax of no greater than 1000.<br>
                2250 is<br>
                      still<br>
                         very high.<br>
<br>
                          &gt; I tried decreasing the emtol value in the em.mdp<br>
               file but it<br>
                         ended with<br>
                          &gt; machine precision.<br>
<br>
                         How far did it converge?  What was Fmax?<br>
<br>
                          &gt; I have read in literature that 5000 steps of<br>
        Steetest<br>
                      Descents run is<br>
                          &gt; required after inserting the protein in the<br>
        bilayer<br>
               which<br>
                      should be<br>
                          &gt; followed by atleast 1000 steps of conjugate<br>
               gradients. How<br>
                      can I<br>
                          &gt; accomplish this ? Is there any parameter to be<br>
               given in the<br>
                         em.mdp file<br>
                          &gt; ? I use steep as the integrator in the mdp<br>
        file for<br>
               energy<br>
                         minimization.<br>
<br>
                         Read the manual.<br>
<br>
                         Whether or not that exact setup is going to be<br>
               &quot;required&quot; is<br>
                      likely<br>
                         system-specific.  I would say that as long as<br>
        your system<br>
                      converges<br>
                         to a stable,<br>
                         negative Epot with a reasonable Fmax (less than<br>
        1000,<br>
               but ideally<br>
                         lower) then<br>
                         you *may* have an appropriate starting structure.<br>
<br>
                         -Justin<br>
<br>
                          &gt; Please help with some suggestions.<br>
                          &gt; Thanks in advance.<br>
                          &gt;<br>
                          &gt; Thanking you,<br>
                          &gt; Pawan<br>
                          &gt;<br>
                          &gt;<br>
                          &gt;<br>
<br>
<br>
<br>
                                   ------------------------------------------------------------------------<br>
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                  --    ========================================<br>
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                  Justin A. Lemkul<br>
                  Graduate Research Assistant<br>
                  ICTAS Doctoral Scholar<br>
                  Department of Biochemistry<br>
                  Virginia Tech<br>
                  Blacksburg, VA<br>
                  jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt;<br>
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                  <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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           --    ========================================<br>
<br>
           Justin A. Lemkul<br>
           Graduate Research Assistant<br>
           ICTAS Doctoral Scholar<br>
           Department of Biochemistry<br>
           Virginia Tech<br>
           Blacksburg, VA<br>
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    --     ========================================<br>
<br>
    Justin A. Lemkul<br>
    Graduate Research Assistant<br>
    ICTAS Doctoral Scholar<br>
    Department of Biochemistry<br>
    Virginia Tech<br>
    Blacksburg, VA<br>
    jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540) 231-9080<br>
    <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
    ========================================<br>
<br>
<br>
</div></div></blockquote><div class="im">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br></div><div class="im">
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