<br>Alright sounds good to me. In order to make it sure once again....I have to do something like this...<div><br></div><div>awk -f atom2cg.awk 1K4C.pdb > 1K4C_cg.pdb</div><div><br></div><div>and then....to get the .gro file....</div>
<div><br></div><div>genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro</div><div><br></div><div>and then......</div><div><br></div><div>grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10</div><div><br></div><div>AM I CORRECT?</div>
<div><br></div><div>Sunny</div><div><div><br></div><div><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 7:44 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">
Hi Justin,<br>
<br>
I am using these commands...<br>
<br>
genbox -cp 1K4C.pdb -box 10 10 10 -o 1K4C.gro<br>
<br>
from here I can get my 1K4C.gro file.<br>
<br>
As far as CG structure of protein is concerned I can produce the CG structure using awk script like this..<br>
<br>
awk -f atom2cg.awk 1K4C.pdb > 1K4C_CG.pdb<br>
<br>
But after getting the CG structure its difficult to get the .itp file for 1K4C_CG.pdb because dssp does not produce .ssd files for CG structure of proteins and if I am not having .ssd file then i cant get 1K4C_CG.itp file so thats why I did not use awk script and I was just doing for the normal protein to test first.<br>
<br>
</blockquote>
<br></div>
You need the awk script to generate the CG structure. You use the atomistic structure to get the .ssd information - you've done this correctly.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Here is the error------------<br>
<br>
grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10<br>
</blockquote>
<br></div>
<snip><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
NOTE 1 [file em.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br>
to 0.3 nm larger than rcoulomb. <br>
<br>
NOTE 2 [file em.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br>
to 0.3 nm larger than rvdw. <br>
</blockquote>
<br></div>
Pay attention to these notes!<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
processing topology...<br>
Generated 0 of the 465 non-bonded parameter combinations<br>
Excluding 1 bonded neighbours molecule type 'Protein' <br>
NOTE 3 [file 1K4C.top, line 15]:<br>
System has non-zero total charge: 4.000000e+00<br>
<br>
<br>
processing coordinates...<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 <br>
Fatal error:<br>
number of coordinates in coordinate file (1K4C.gro, 4534)<br>
does not match topology (1K4C.top, 1166) <br>
<br>
</blockquote>
<br></div>
Now this makes sense. You are using an atomistic structure (1K4C.gro) with a CG topology. The structure input into grompp should be the CG structure that comes from the awk script.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
<br>
<br>
<br>
On Tue, Aug 18, 2009 at 7:24 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>
Ok. Thanks but I am doing a small test to make the .top file and<br>
.gro files of fresh 1K4C protein structure without removing<br>
anything but when I run my grommp command to minimize it as I<br>
asked earlier as well it says number of atoms in the .top are<br>
not equal to .top file and as you said that without adding any<br>
other molecule I just have to fix the [molecules] section, but<br>
it doesn't fix.<br>
<br>
here are some details of my .top file which I created on my own<br>
after getting the 1K4C.itp file. I got 1K4C.itp file something<br>
like this..<br>
<br>
grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq)<br>
dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp)<br>
dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd)<br>
<br>
seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp<br>
<br>
<br>
<snip><br>
<br>
<br>
and after that I produce my 1K4C.gro file from genbox or<br>
editconf and then when i run the command grommp it says that<br>
number of atoms in .gro<br>
<br>
<br>
What commands are you giving genbox/editconf? You've never invoked<br>
the awk script that converts an atomistic protein structure to CG<br>
(provided by the MARTINI folks). Could that be the cause of the<br>
disconnect? Without seeing the actual error message, the best<br>
anyone can do is guess.<br>
<br>
-Justin<br>
<br>
file are unequal to .top file. Since I am doing the simulation<br>
in vacuum I cannot add anything else. Don't know how to proceed.<br>
<br>
Thanks,<br>
<br>
Sunny<br>
<br>
On Tue, Aug 18, 2009 at 7:00 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><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>
Hi all,<br>
<br>
Is there anyway I can generate the .gro file from .top file<br>
without using the command pdb2gmx and editconf?<br>
<br>
<br>
A .top file is a topology - atomic descriptions; a .gro is a<br>
coordinate file. They are unrelated and therefore cannot be<br>
inter-converted.<br>
<br>
-Justin<br>
<br>
<br>
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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">
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<br>
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Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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<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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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