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>Here is the error------------<br><br>grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10<br><br> :-) G R O M A C S (-: <br><br> Gromacs Runs One Microsecond At Cannonball Speeds<br>
<br> :-) VERSION 4.0.5 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands. <br>
Copyright (c) 2001-2008, The GROMACS development team, <br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information. <br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License <br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version. <br>
<br> :-) grompp (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f em.mdp Input, Opt! grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br> -c 1K4C.gro Input Structure file: gro g96 pdb tpr tpb tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -n index.ndx Input, Opt. Index file <br> -p 1K4C.top Input Topology file <br>
-pp processed.top Output, Opt. Topology file <br> -o topol.tpr Output Run input file: tpr tpb tpa <br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt <br>
-e ener.edr Input, Opt. Energy file: edr ene <br><br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit <br>
-nice int 0 Set the nicelevel <br>-[no]v bool yes Be loud and noisy <br>-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br>
sites <br>-maxwarn int 10 Number of allowed warnings during input processing<br>-[no]zero bool no Set parameters for bonded interactions without <br>
defaults to zero instead of generating an error <br>-[no]renum bool yes Renumber atomtypes and minimize number of <br> atomtypes <br>
<br>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp' <br>Replacing old mdp entry 'unconstrained_start' by 'continuation'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#<br>
checking input for internal consistency... <br><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><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><br>processing topology...<br>
Generated 0 of the 465 non-bonded parameter combinations<br>Excluding 1 bonded neighbours molecule type 'Protein' <br><br>NOTE 3 [file 1K4C.top, line 15]:<br> System has non-zero total charge: 4.000000e+00<br> <br>
<br><br>processing coordinates...<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.5 <br>Source code file: grompp.c, line: 362 <br><br>
Fatal error:<br>number of coordinates in coordinate file (1K4C.gro, 4534)<br> does not match topology (1K4C.top, 1166) <br><br><br><br><br><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 7:24 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>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
<br>
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..<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>
</blockquote>
<br></div>
<snip><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;">
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 <br>
</blockquote>
<br></div>
What commands are you giving genbox/editconf? You've never invoked the awk script that converts an atomistic protein structure to CG (provided by the MARTINI folks). Could that be the cause of the disconnect? Without seeing the actual error message, the best anyone can do is guess.<br>
<br>
-Justin<br>
<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">
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.<br>
<br>
Thanks,<br>
<br>
Sunny<br>
<br></div><div class="im">
On Tue, Aug 18, 2009 at 7:00 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>
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>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><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>> | (540) 231-9080<div class="im"><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>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></blockquote><div><div></div><div class="h5">
<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>
<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>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>