I did the same but again i get the same error..something like this<br><br><span style="color: rgb(255, 0, 0);">awk -f atom2cg_v2.1tryout.awk 1K4C.pdb > 1K4C_cg.pdb</span><br> <br>(This generated 1K4C_cg.pdb file)<br><br>
<span style="color: rgb(255, 0, 0);">genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro</span><br><br>(produced 1K4C_cg.gro)<br><br>GROningen MAchine for Chemical Simulation<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> :-) genbox (-:<br><br>Option Filename Type Description<br>
------------------------------------------------------------<br> -cp 1K4C_cg.pdb Input, Opt! Structure file: gro g96 pdb tpr tpb tpa<br> -cs spc216.gro Input, Opt., Lib. Structure file: gro g96 pdb tpr tpb tpa<br>
-ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa <br> -o 1K4C_cg.gro Output Structure file: gro g96 pdb <br> -p topol.top In/Out, Opt. Topology file <br>
<br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit <br>-nice int 19 Set the nicelevel <br>
-box vector 10 10 10 box size <br>-nmol int 0 no of extra molecules to insert<br>-try int 10 try inserting -nmol*-try times <br>-seed int 1997 random generator seed <br>
-vdwd real 0.105 default vdwaals distance <br>-shell real 0 thickness of optional water layer around solute<br>-maxsol int 0 maximum number of solvent molecules to add if <br>
they fit in the box. If zero (default) this is <br> ignored <br>-[no]vel bool no keep velocities from input solute and solvent <br>
<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>WARNING: masses will be determined based on residue and atom names, <br> this can deviate from the real mass of the atom type <br>
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat <br>Entries in atommass.dat: 178 <br>WARNING: vdwradii will be determined based on residue and atom names, <br>
this can deviate from the real mass of the atom type <br>Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat <br>Entries in vdwradii.dat: 28 <br>
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat <br>Entries in dgsolv.dat: 7 <br>Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>
Entries in electroneg.dat: 71 <br>Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat <br>Entries in elements.dat: 218 <br>
Reading solute configuration <br>MEMBRANE PROTEIN <br>Containing 1127 atoms in 534 residues <br>
Initialising van der waals distances... <br>Writing generated configuration to 1K4C_cg.gro <br>MEMBRANE PROTEIN <br>
<br>Output configuration contains 1127 atoms in 534 residues<br>Volume : 1000 (nm^3) <br>Density : 53.8545 (g/l) <br>Number of SOL molecules: 0 <br>
<br><br>gcq#69: "I Want to Know Right Now" (Meatloaf)<br><br><br>After that ;;;;;;;;;;;;;;;;;;;;;;;<br><br><span style="color: rgb(204, 0, 0);">grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10</span><br><br>
:-) G R O M A C S (-: <br><br> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon<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_cg.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.9#<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><span style="color: rgb(255, 0, 0);">number of coordinates in coordinate file (1K4C_cg.gro, 1127)</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> does not match topology (1K4C.top, 1166)</span><br>-------------------------------------------------------<br><br><br><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 7:54 PM, sunny mishra <span dir="ltr"><<a href="mailto:mishra.sunny@gmail.com">mishra.sunny@gmail.com</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;"><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><font color="#888888"><div>Sunny</div></font><div><div></div><div class="h5"><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" target="_blank">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><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;">
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><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>
<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>
<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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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>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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<br>
-- <br>
========================================<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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</div></div></blockquote></div><br>