Dear Dr.Justin<br>Yes,I know,it deleted some lipids according to inflateGRO script in the first timethat I used perl command.<br>Besides: <br>I did iteration 25 times correctly,and no addition or doubling was occured.<br>I used the same commands of 25th iteration.of course I changed numberes from 25 to 26 in commands.<br>
I think it is because I have compacted my lipids more than it is required.<br><br>my commands are as below:<br>after doing EM for output of 25th iteration(its output were EM-inflate-26.*) I entered :<br><br>trjconv -f EM-inflate-26.trr -s EM-inflate-26.tpr -o EM-inflate-26-trj.gro -pbc mol -ur compact<br>
perl inflategro EM-inflate-26-trj.gro 0.95 DPPC 0 system_shrink26.gro 5 area_shrink26.dat<br>grompp -f minim-strong.mdp -c system_shrink26.gro -p topol.top -o EM-inflate-27.tpr<br>
<br>thanks in advance for your reply<br><br><br><div class="gmail_quote">On Mon, Mar 7, 2011 at 5:42 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all<br>
<br>
I am doing Membrane -protein tutorial.<br>
Actually I did each step carefully,I could score down my lipids 26 times.<br>
But there were two problems:<br>
1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said<br>
2-I tried to do more iteration to make closer my area per lipid to 71,But I get the following error:<br>
Program grompp, VERSION 4.0.7<br>
Source code file: ../../../../src/kernel/grompp.c, line: 362<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file (system_shrink26.gro, 12876)<br>
does not match topology (topol.top, 6438)<br>
<br>
I checked and I found program has added some additional DPPC molecules to my system!!<br>
</blockquote>
<br></div>
InflateGRO does not add lipids, it deletes them. Whatever you've done has exactly doubled the system. You've managed to concatenate coordinate files or otherwise manipulate it in some nonsensical way. Without seeing the command you used it's impossible to say.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Besides I get 32 A area per lipid for this step!!!<br>
<br>
Please let me know what is the reason.<br>
Thanks in advance<br>
Mohsen<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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