Ok. Thanks but I am doing a small test to make the .top file and .gro files of fresh 1K4C protein structure without removing anything but when I run my grommp command to minimize it as I asked earlier as well it says number of atoms in the .top are not equal to .top file and as you said that without adding any other molecule I just have to fix the [molecules] section, but it doesn't fix.<div>
<br></div><div> here are some details of my .top file which I created on my own after getting the 1K4C.itp file. I got 1K4C.itp file something like this..</div><div><br></div><div>grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq)</div>
<div>dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp)</div><div>dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd)</div><div><br></div><div>seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp</div><div><br></div><div>My topology file looks like this</div>
<div><br></div><div>; Include forcefield parameters</div><div>#include "martini_v2.1.itp"</div><div><br></div><div>; Include protein</div><div>#include "1K4C.itp"</div><div><br></div><div>[ system ]</div>
<div>; Name</div><div>Membrane Protein</div><div><br></div><div>[ molecules ]</div><div>; compound # mols</div><div>Protein 1</div><div><br></div><div>and after that I produce my 1K4C.gro file from genbox or editconf and then when i run the command grommp it says that number of atoms in .gro file are unequal to .top file. Since I am doing the simulation in vacuum I cannot add anything else. Don't know how to proceed.</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Sunny</div><div><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 7:00 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 all,<br>
<br>
Is there anyway I can generate the .gro file from .top file without using the command pdb2gmx and editconf?<br>
<br>
</blockquote>
<br></div>
A .top file is a topology - atomic descriptions; a .gro is a coordinate file. They are unrelated and therefore cannot be inter-converted.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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