Hi, Justin: <br>I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal error:<br><br>Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms<br> while sorting atoms. Maybe different protonation state.<br>
Remove this hydrogen or choose a different protonation state.<br> Option -ignh will ignore all hydrogens in the input.<br>If I creat one ( CH4), it said that : <br>Residue 'CH4' not found in residue topology database.<br>
<br>my pdb file for methane pair is ( I created from MOE), original residue name is *, now I change to CH4: <br>REMARK 99 MOE v2007.09 (Chemical Computing Group Inc) Mon Oct 20 12:31:39 2008<br>HETATM 1 C CH4 1 -0.415 -0.007 0.005 0.00 0.00 C<br>
HETATM 2 H2 CH4 1 -0.778 0.720 0.731 0.00 0.00 H<br>HETATM 3 H3 CH4 1 -0.778 -0.999 0.271 0.00 0.00 H<br>HETATM 4 H4 CH4 1 -0.778 0.259 -0.988 0.00 0.00 H<br>
HETATM 5 H1 CH4 1 0.675 -0.007 0.005 0.00 0.00 H<br>HETATM 6 C CH4 2 9.588 -0.007 0.005 0.00 0.00 C<br>HETATM 7 H1 CH4 2 10.678 -0.007 0.005 0.00 0.00 H<br>
HETATM 8 H2 CH4 2 9.225 0.720 0.731 0.00 0.00 H<br>HETATM 9 H3 CH4 2 9.225 -0.999 0.271 0.00 0.00 H<br>HETATM 10 H4 CH4 2 9.225 0.259 -0.988 0.00 0.00 H<br>
CONECT 1 2 3 4 5<br>CONECT 6 7 8 9 10<br>END<br><br>What kind of residue name I should put there? thanks lot. <br>-Xianghong Qi<br><br><br><div class="gmail_quote">On Wed, Oct 22, 2008 at 9:56 AM, xianghong qi <span dir="ltr"><<a href="mailto:xianghong001@gmail.com">xianghong001@gmail.com</a>></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;">Thanks so much , Justin. I will try. <br><font color="#888888">-Xianghong Qi</font><div><div>
</div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></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><br>
<br>
xianghong qi wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks, so how to edit a residue name ? I am confused. sorry about such simple question. <br>
</blockquote>
<br></div>
Use a text editor. Be sure to keep the formatting right when doing so:<br>
<br>
<a href="http://www.wwpdb.org/documentation/format32/sect9.html" target="_blank">http://www.wwpdb.org/documentation/format32/sect9.html</a><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;">
-Xianghong Qi<div><br>
<br>
On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
xianghong qi wrote:<br>
<br>
Hello, everyone,<br>
I want to create a pdb file for methane pair . I can make<br>
methane pair from MOE and then save to pdb file format without<br>
any residue name there.<br>
The question is that I can't convert pdb file to .gro file from<br>
gromacs without residue name. Anyone has any idea about this<br>
question. I appreciate<br>
your help.<br>
<br>
<br>
You don't need a .gro file for itself.. see<br>
<a href="http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file" target="_blank">http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file</a><br>
<br>
You'll need a residue name to get a topology defined, so edit one in.<br>
<br>
Mark<br>
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Virginia Tech<br>
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