Hi Justin,<br><br>Thanks for the reply and here is the following which I am doing. I would appreciate if you can point out my errors.<br><br><br>1) I am working on 1K4C (KcSA) and i downloaded that from <a href="http://www.pdb.org">www.pdb.org</a> and after that I cleaned the PBD file, removed all the HETATOMS and ATOMS with ligand A & B and also removed the TER atoms. So my cleaned PDB file i.e. (1K4C_clean.pdb) consists of atoms with ligands C and #of atoms are 765.<br>
<br>2) After getting the 1K4C_clean.pdb I converted the atomic structure to CG structure using awk script...something like this<br><br><span style="color: rgb(0, 153, 0);">awk -f atom2cg.awk 1K4C_clean.pdb > 1K4C_cleanCG.pdb</span><br>
<br>3) Then I got the sequence of 1K4C_clean.pdb using vmd and saved that as 1K4C_clean.txt and with the help of the following command I got the .seq file...<br><br><span style="color: rgb(0, 153, 0);">grep -A 1 1K4C_clean 1K4C_clean.txt > 1K4C_clean.seq</span><br>
<br>4) Then using dssp I got the .ssd file for 1K4C_clean.pdb....<br><br><span style="color: rgb(0, 153, 0);">dsspcmbi 1K4C_clean.pdb 1K4C_clean.dssp</span><br style="color: rgb(0, 153, 0);"><span style="color: rgb(0, 153, 0);">dssp2ssd.py 1K4C_clean.dssp -o 1K4C_clean.ssd</span><br>
<br>5) After preparing the secondary structure files I generated the MARTINI topology files like this :<br><br><span style="color: rgb(0, 153, 0);">seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp</span><br><br>
6) The next step is to make the topology file and I made like this.....<br><br>; Include Martini Topology<br>#include "martini_v2.1.itp"<br><br>; Include protein topology<br>#include "1K4C_clean.itp"<br>
<br><br>[ system ]<br>; Name<br>Membrane Protein<br><br>[ molecules ]<br>; compound #mols<br>Protein 1<br><br>7) Then I made the .gro file using genbox.....<br><br><span style="color: rgb(0, 153, 0);">genbox -cp 1K4C_cleanCG.pdb -box 10 10 10 -o 1K4C_cleanCG.gro</span><br>
<br>(In the previous email as you said that I need to make the .gro file of CG structure of protein so I used 1K4C_cleanCG.pdb)<br><br>8) Now I want to minimize the system.....<br><br><span style="color: rgb(0, 153, 0);">grompp -f em.mdp -c 1K4C_cleanCG.gro -p 1K4C_clean.top -maxwarn 10</span><br>
<br>and then error comes...........<br><br>:-) G R O M A C S (-: <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> :-) 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_cleanCG.pdb 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_clean.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_clean.top, line 15]:<br> System has non-zero total charge: 2.000000e+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><span style="color: rgb(255, 0, 0);">Fatal error:</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">number of coordinates in coordinate file (1K4C_cleanCG.pdb, 209)</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"> does not match topology (1K4C_clean.top, 216)</span><br>
-------------------------------------------------------<br><br>I don't know where I have done the mistake...your help will be highly appreciable in this case. <br><br>Thanks a lot,<br><br>Sunny<br><br><br><br><br><div class="gmail_quote">
On Wed, Aug 19, 2009 at 6:09 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;">
Hi,<br>
<br>
I checked both the files they match exactly but still I get the same error message that .gro file and .top file dnt match. I dnt know how to proceed now.<br>
<br>
</blockquote>
<br></div>
Well, something has to be wrong, or else grompp wouldn't complain. You say you've checked the .top, but have you also checked the contents of any relevant .itp files that are #included within it?<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;">
Sunny<div class="im"><br>
<br>
On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra <<a href="mailto:mishra.sunny@gmail.com" target="_blank">mishra.sunny@gmail.com</a> <mailto:<a href="mailto:mishra.sunny@gmail.com" target="_blank">mishra.sunny@gmail.com</a>>> wrote:<br>
<br>
Ok..I will see that and let you know. Thanks for the help though.<br>
<br>
Sunny<br>
<br>
<br>
On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham<br></div><div><div></div><div class="h5">
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
sunny mishra wrote:<br>
<br>
I did the same but again i get the same error..something<br>
like this<br>
<br>
awk -f atom2cg_v2.1tryout.awk 1K4C.pdb > 1K4C_cg.pdb<br>
<br>
(This generated 1K4C_cg.pdb file)<br>
<br>
genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro<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<br>
Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The<br>
Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development<br>
team,<br>
check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more<br>
information.<br>
<br>
This program is free software; you can redistribute<br>
it and/or<br>
modify it under the terms of the GNU General Public<br>
License<br>
as published by the Free Software Foundation; either<br>
version 2<br>
of the License, or (at your option) any later<br>
version.<br>
<br>
:-) genbox (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-cp 1K4C_cg.pdb Input, Opt! Structure file: gro g96<br>
pdb tpr tpb tpa<br>
-cs spc216.gro Input, Opt., Lib. Structure file: gro<br>
g96 pdb tpr tpb<br>
tpa<br>
-ci insert.gro Input, Opt. Structure file: gro g96<br>
pdb tpr tpb<br>
tpa<br>
-o 1K4C_cg.gro Output Structure file: gro g96<br>
pdb<br>
-p topol.top In/Out, Opt. Topology<br>
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<br>
layer around solute<br>
-maxsol int 0 maximum number of solvent<br>
molecules to add if<br>
they fit in the box. If zero<br>
(default) this is<br>
ignored<br>
-[no]vel bool no keep velocities from input<br>
solute and solvent<br>
<br>
Opening library file<br>
/usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom<br>
names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file<br>
/usr/local/gromacs/share/gromacs/top/atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and<br>
atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file<br>
/usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file<br>
/usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file<br>
/usr/local/gromacs/share/gromacs/top/electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file<br>
/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>
grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10<br>
<br>
:-) G R O M A C S<br>
(-:<br>
<br>
Gallium Rubidium Oxygen Manganese Argon Carbon<br>
Silicon<br>
<br>
:-) VERSION 4.0.5 (-:<br>
<br>
<br>
Written by David van der Spoel, Erik Lindahl, Berk<br>
Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The<br>
Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development<br>
team,<br>
check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more<br>
information.<br>
<br>
This program is free software; you can redistribute<br>
it and/or<br>
modify it under the terms of the GNU General Public<br>
License<br>
as published by the Free Software Foundation; either<br>
version 2<br>
of the License, or (at your option) any later<br>
version.<br>
<br>
:-) grompp (-:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-f em.mdp Input, Opt! grompp input file with MD<br>
parameters<br>
-po mdout.mdp Output grompp input file with MD<br>
parameters<br>
-c 1K4C_cg.gro Input Structure file: gro g96 pdb<br>
tpr tpb tpa<br>
-r conf.gro Input, Opt. Structure file: gro g96 pdb<br>
tpr tpb tpa<br>
-rb conf.gro Input, Opt. Structure file: gro g96<br>
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:<br>
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<br>
this time.<br>
-[no]rmvsbds bool yes Remove constant bonded<br>
interactions with virtual<br>
sites<br>
-maxwarn int 10 Number of allowed warnings<br>
during input<br>
processing<br>
-[no]zero bool no Set parameters for bonded<br>
interactions<br>
without<br>
defaults to zero instead of<br>
generating an<br>
error<br>
-[no]renum bool yes Renumber atomtypes and minimize<br>
number<br>
of<br>
<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<br>
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<br>
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_cg.gro, 1127)<br>
does not match topology (1K4C.top, 1166)<br>
-------------------------------------------------------<br>
<br>
<br>
That's a pretty explicit error message. Go and look at the<br>
molecule and atom ordering in the two files and see where they<br>
don't match.<br>
<br>
Mark<br>
<br>
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------------------------------------------------------------------------<div class="im"><br>
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<br><div class="im">
-- <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></div><div><div></div><div class="h5">
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