Alright. I have done this....I have made another lipid_newbox.gro file and wrote same box vectors as of lipid.gro file<div><br></div><div>For LIPID :</div><div><br></div><div>editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160</div>
<div><br></div><div>For Protein :</div><div><br></div><div>editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820 6.59160</div><div><br></div><div>Then cat the system and made system.gro file and did inflategro of the system.gro file. Do you think this is the correct way and now when I visualize this in VMD the protein is shifted little upwards but it is at the center of the lipid.</div>
<div><br></div><div>Sunny<br> <br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 4:59 PM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
No. But in order to do that with lipid.gro what co-ordinates should I have to take?<br>
<br>
</blockquote>
<br></div>
I think you need to differentiate between "coordinates" and "box vectors." You should center the molecule in the box (defined by the vectors in the last line of the .gro file). I assumed you were specifying these box vectors with -box.<br>
<br>
So, for both the protein and the lipid coordinate files, you need to use<br>
<br>
editconf -c -box (x, y, z from .gro file)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
sunny mishra wrote:<br>
<br>
okk...here are the commands which I am givng...<br>
<br>
editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box<br>
13.29820 13.29820 6.59160<br>
<br>
I get the 1SU4_newbox.gro which has co-ordinates 13.29820<br>
13.29820 6.59160<br>
<br>
<br>
Have you done the same with lipid.gro? If the protein and the lipid<br>
are in different coordinate systems (i.e., lipid.gro centered at the<br>
origin and protein centered within the box, which has its corner<br>
placed at the origin) then you will have a problem.<br>
<br>
-Justin<br>
<br>
cat 1SU4_newbox.gro lipid.gro > system..gro<br>
<br>
Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160<br>
<br>
now inflategro:<br>
<br>
inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5<br>
<br>
Now when i visualize my output file in VMD then protein and<br>
lipid are seperated and even after i scale it to .95 they dnt<br>
meet....they are still apart, I was hoping that lipid will be<br>
scaled and protein shud have remained in the center of the lipid<br>
but that doesn't happen. I hope you got my question<br>
<br>
On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
sunny mishra wrote:<br>
<br>
Yes I did the same and when I see my system.gro file it<br>
gives me<br>
the dimensions of the protein box half of the lipid<br>
bilayer box<br>
so that means it should now be set in the center of the lipid<br>
bilayer. But after<br>
<br>
<br>
I don't understand what you mean.<br>
<br>
<br>
that when I run the inflategro script and see my output<br>
file the<br>
protein and lipid are separated and I dnt know why?<br>
<br>
<br>
Can you post the actual commands you're using?<br>
<br>
-Justin<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<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>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<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>
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