<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
abdullah ahmed wrote:<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">
Hello,<br>
<br>
I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do:<br>
<br></div>
1. Apply pdb2gmx to the pdb file to convert it to .gro and .top<br>
(pdb2gmx -f -p -o)<br>
2. Run editconf to define the box (editconf -d 1)<br>
3. run gromp and mdrun for the minimization<br></blockquote></blockquote><div>use mdrun -c . It will give you the required pdb file<br><br>Chandan <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
4. Run editconf to re-convert back to pdb<div class="im"><br>
<br>
<br>
Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info?<br>
<br>
</div></blockquote>
<br>
What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you in advance,<br>
Abdullah<br>
<br>
<br>
</blockquote>
<br></div>
-- <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>
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