Thank you very much<br><br><div class="gmail_quote">22 Ocak 2011 23:07 tarihinde Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
please look at the attached file<br>
<br>
</blockquote>
<br></div>
I had no problem making a topology.<br>
<br>
$ pdb2gmx -f 3MOA.pdb -ter<br>
<br>
...<br>
Using the Gromos43a1 force field in directory gromos43a1.ff<br>
...<br>
Select start terminus type for GLU-659<br>
 0: NH3+<br>
 1: NH2<br>
 2: None<br>
0<br>
Start terminus GLU-659: NH3+<br>
Select end terminus type for NH2-671<br>
 0: COO-<br>
 1: COOH<br>
 2: None<br>
2<br>
End terminus NH2-671: None<br>
Checking for duplicate atoms....<br>
Now there are 13 residues with 139 atoms<br>
Chain time...<br>
...<br>
Select start terminus type for LEU-2<br>
 0: NH3+<br>
 1: NH2<br>
 2: None<br>
0<br>
Start terminus LEU-2: NH3+<br>
Select end terminus type for CYS-214<br>
 0: COO-<br>
 1: COOH<br>
 2: None<br>
0<br>
End terminus CYS-214: COO-<br>
...<br>
Select start terminus type for ARG-1<br>
 0: NH3+<br>
 1: NH2<br>
 2: None<br>
0<br>
Start terminus ARG-1: NH3+<br>
Select end terminus type for ASP-217<br>
 0: COO-<br>
 1: COOH<br>
 2: None<br>
0<br>
End terminus ASP-217: COO-<br>
...<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
22 Ocak 2011 22:54 tarihinde 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; yazdı:<div class="im">
<br>
<br>
<br>
<br>
    ahmet yıldırım wrote:<br>
<br>
        Dear Justin,<br>
<br>
        I manually specify termini.  I choosed &quot;None&quot; but I have the<br>
        same error.<br>
<br>
        Fatal error:<br>
        atom C not found in residue 13NH2 while combining tdb and rtp<br>
<br>
<br>
    Please post your .pdb file.<br>
<br>
    -Justin<br>
<br>
<br>
        22 Ocak 2011 00:45 tarihinde Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt; &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; yazdı:<br>
<br>
<br>
<br>
<br>
           ahmet yıldırım wrote:<br>
<br>
               Dear justin,<br>
<br>
               I looked at the pdb file. No NH2 reside contains carbon atom.<br>
<br>
               What should I do?<br>
<br>
<br>
           In this case, you need to manually specify termini.  Choose<br>
        &quot;None&quot;<br>
           to allow your capping groups to be built properly.<br>
<br>
           -Justin<br>
<br>
<br>
               22 Ocak 2011 00:18 tarihinde 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></div><div class="im">
        &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>
<br></div>
               &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; yazdı:<div><div></div><div class="h5">
<br>
<br>
<br>
<br>
<br>
                  ahmet yıldırım wrote:<br>
<br>
                      I think I need to edit the aminoacids.rtp file in<br>
               gromos43a1.ff<br>
                      folder as far as I understand from mailing list. I am<br>
               using 43a1<br>
                      forcefield. I do not understand what kind of changes<br>
               should I do.<br>
<br>
<br>
                  You do not need to modify the .rtp file, you need to<br>
        modify your<br>
                  coordinate file, as I said before.  The fatal error<br>
        indicates<br>
               that<br>
                  you have included a C atom in an NH2 residue, which is<br>
        just a<br>
                  neutral amine and contains no carbon, as should be<br>
        clear from the<br>
                  .rtp file.<br>
<br>
                  -Justin<br>
<br>
                      *the aminoacids.rtp file:*<br>
<br>
                      [ ACE ]<br>
                       [ atoms ]<br>
                         CA   CH3   0.000     0<br>
                          C     C   0.380     1<br>
                          O     O  -0.380     1<br>
                       [ bonds ]<br>
                          C    CA   gb_26<br>
                          C     O   gb_4<br>
                          C    +N   gb_9<br>
                       [ angles ]<br>
                        CA     C     O    ga_30<br>
                        CA     C    +N    ga_18<br>
                         O     C    +N    ga_32<br>
                       [ impropers ]<br>
                         C    CA    +N     O    gi_1<br>
<br>
                      [ NH2 ]<br>
                       [ atoms ]<br>
                          N    NT   -0.83    0<br>
                          H1    H   0.415    0<br>
                          H2    H   0.415   0<br>
                       [ bonds ]<br>
                           N    H1  gb_2<br>
                           N    H2  gb_2       -C    N   gb_8<br>
                       [ angles ]<br>
                          -O -C N  ga_32<br>
                          -CA -C N ga_18<br>
                          -C N H1  ga_22<br>
                          -C N H2  ga_22<br>
                          H1 N H2  ga_23<br>
                       [ dihedrals ]<br>
                         -CA -C N H1 gd_4<br>
                       [ impropers ]<br>
                         -C -O N -CA gi_1<br>
                          N  H1 H2  -C gi_1<br>
<br>
                      [ ALA ]<br>
                       [ atoms ]<br>
                         N     N    -0.28000     0<br>
                         H     H     0.28000     0<br>
                        CA   CH1     0.00000     1<br>
                        CB   CH3     0.00000     1<br>
                         C     C       0.380     2<br>
                         O     O      -0.380     2<br>
                       [ bonds ]<br>
                         N     H    gb_2       N    CA    gb_20     CA            C           gb_26<br>
                           C     O    gb_4       C    +N    gb_9      CA<br>
           CB<br>
                  gb_26          2011/1/21 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;<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;<br>
<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;&gt;<br>
<br>
<br>
<br>
<br>
<br>
                         ahmet yıldırım wrote:<br>
<br>
                             Dear users,<br>
<br>
                             Gromacs 4.5.3<br>
                             pdb2gmx -f xxx.pdb -water spc<br>
                             select Force Field:9<br>
                             *Fatal error:*<br>
                             atom C not found in buiding block 13NH2 while<br>
               combining<br>
                      tdb and rtp<br>
                             For more information and tips for<br>
        troubleshooting,<br>
               please<br>
                      check<br>
                             the GROMACS<br>
                             website at<br>
        <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
                             How can I fixed this error?<br>
<br>
<br>
                         You have a carbon atom in a residue that should<br>
        only<br>
               contain NH2.<br>
                          Refer to the .rtp file for what is expected,<br>
        then make a<br>
                      suitable<br>
                         structure that conforms to those requirements.<br>
<br>
                         This has been asked and answered hundreds of<br>
        times, so<br>
               please<br>
                      make<br>
                         use of the mailing list search.  You would have<br>
        gotten<br>
               your<br>
                      answer<br>
                         in minutes rather than hours.<br>
<br>
                         -Justin<br>
<br>
<br>
                             Thanks in advance<br>
<br>
<br>
                             --         Ahmet YILDIRIM<br>
<br>
<br>
                         --     ========================================<br>
<br>
                         Justin A. Lemkul<br>
                         Ph.D. Candidate<br>
                         ICTAS Doctoral Scholar<br>
                         MILES-IGERT Trainee<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;<br>
        &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>
               &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
<br>
                      231-9080<br>
<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>
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<br>
<br>
<br>
                      --         Ahmet YILDIRIM<br>
<br>
<br>
                  --     ========================================<br>
<br>
                  Justin A. Lemkul<br>
                  Ph.D. Candidate<br>
                  ICTAS Doctoral Scholar<br>
                  MILES-IGERT Trainee<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>
        &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
               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>
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<br>
<br>
<br>
               --         Ahmet YILDIRIM<br>
<br>
<br>
           --     ========================================<br>
<br>
           Justin A. Lemkul<br>
           Ph.D. Candidate<br>
           ICTAS Doctoral Scholar<br>
           MILES-IGERT Trainee<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; | (540)<br>
        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>
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<br>
<br>
<br>
<br>
        --         Ahmet YILDIRIM<br>
<br>
<br>
    --     ========================================<br>
<br>
    Justin A. Lemkul<br>
    Ph.D. Candidate<br>
    ICTAS Doctoral Scholar<br>
    MILES-IGERT Trainee<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>
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<br>
<br>
<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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>
-- <br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don&#39;t post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>