<br>Alright. Sounds good to me. let me check that out and i will let you know the progress.<div><br></div><div>Thanks,</div><div><br></div><div>Sunny</div><div><div><br></div><div><br><div class="gmail_quote">On Wed, Aug 19, 2009 at 7:19 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 Mark and Justin,<br>
<br>
Thanks for the valuable advise and I want to do the last test but before I proceed I just want to make sure If I am doing everything correct.<br>
<br>
I got the 1K4C_cleanCG.seq file using grep command like this<br>
<br>
grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq<br>
<br>
Now my next step is to get the .ssd file for 1K4C_cleanCG.pdb which I cannot get and in that case I have to use 1K4C_clean.pdb in order to get .ssd file.<br>
<br>
And If i am correct here then my next step would be to get the .itp file for 1K4C_cleanCG. So my last question is that when I will use seq2itp.pl script which .seq file should I use and which .ssd file should I use to get the output .itp file. I mean this....<br>
<br>
seq2itp.pl 1K4C_cleanCG.seq 1K4C_clean.ssd > 1K4C_cleanCG.itp<br>
<br>
OR<br>
seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp<br>
<br>
In the first command I don't think I can get the .ssd file( 1K4C_cleanG.ssd ) so thats why I am using 1K4C_clean.ssd. Now I dnt know if I am doing this wrong or correct but before proceeding i want to ask you guys to correct me at this point.<br>
<br>
</blockquote>
<br></div>
The .seq file should not depend at all on anything to do with the structure; the amino acid sequence is invariant. You can download the FASTA sequence from the PDB and use that (accounting for any missing terminal residues); it shouldn't make a difference.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
<br>
Sunny<div class="im"><br>
<br>
On Wed, Aug 19, 2009 at 6:54 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>
In addition to everything Mark said, also realize that there may be<br>
a fundamental problem in everything you are doing: there are missing<br>
atoms in the original 1K4C structure. If you have not modeled them<br>
back in, the appropriate CG particles will not necessarily all be<br>
placed in your CG structure, but the topology will be written such<br>
that it expects all the correct atoms to be there.<br>
<br>
At first glance, Arg117 is going to cause headaches - it is missing<br>
all atoms beyond CB, and since CG and NE are necessary for MARTINI's<br>
definition of an ARG residue, you can bet this will be a problem.<br>
<br>
-Justin<br>
<br>
<br>
Mark Abraham wrote:<br>
<br>
sunny mishra wrote:<br>
<br>
Hi Justin,<br>
<br>
Thanks for the reply and here is the following which I am<br>
doing. I would<br>
appreciate if you can point out my errors.<br>
<br>
<br>
1) I am working on 1K4C (KcSA) and i downloaded that from<br></div>
<a href="http://www.pdb.org" target="_blank">www.pdb.org</a> <<a href="http://www.pdb.org" target="_blank">http://www.pdb.org</a>> and<div><div></div><div class="h5"><br>
after that I cleaned the PBD file, removed all the HETATOMS<br>
and ATOMS with<br>
ligand A & B and also removed the TER atoms. So my cleaned<br>
PDB file i.e.<br>
(1K4C_clean.pdb) consists of atoms with ligands C and #of<br>
atoms are 765.<br>
<br>
2) After getting the 1K4C_clean.pdb I converted the atomic<br>
structure to CG<br>
structure using awk script...something like this<br>
<br>
awk -f atom2cg.awk 1K4C_clean.pdb > 1K4C_cleanCG.pdb<br>
<br>
<br>
Here you create 1K4C_cleanCG.pdb<br>
<br>
3) Then I got the sequence of 1K4C_clean.pdb using vmd and<br>
saved that as<br>
1K4C_clean.txt and with the help of the following command I<br>
got the .seq<br>
file...<br>
<br>
<br>
But below you create your .itp starting from "1K4C_clean", which<br>
at least means you haven't copied your correct grep line, and<br>
might indicate the mismatch between your structure and topology.<br>
<br>
grep -A 1 1K4C_clean 1K4C_clean.txt > 1K4C_clean.seq<br>
<br>
4) Then using dssp I got the .ssd file for 1K4C_clean.pdb....<br>
<br>
dsspcmbi 1K4C_clean.pdb 1K4C_clean.dssp<br>
dssp2ssd.py 1K4C_clean.dssp -o 1K4C_clean.ssd<br>
<br>
5) After preparing the secondary structure files I generated<br>
the MARTINI<br>
topology files like this :<br>
<br>
seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp<br>
<br>
6) The next step is to make the topology file and I made<br>
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>
genbox -cp 1K4C_cleanCG.pdb -box 10 10 10 -o 1K4C_cleanCG.gro<br>
<br>
(In the previous email as you said that I need to make the<br>
.gro file of CG<br>
structure of protein so I used 1K4C_cleanCG.pdb)<br>
<br>
<br>
A .gro file is almost never essential. A structure file with a<br>
suitable periodic box can be.<br>
<br>
8) Now I want to minimize the system.....<br>
<br>
grompp -f em.mdp -c 1K4C_cleanCG.gro -p 1K4C_clean.top<br>
-maxwarn 10<br>
<br>
and then error comes...........<br>
<br>
:-) G R O M A C S<br>
(-:<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>
:-) 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_cleanCG.pdb Input Structure file: gro g96<br>
pdb 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_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:<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.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<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_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>
Fatal error:<br>
number of coordinates in coordinate file (1K4C_cleanCG.pdb, 209)<br>
does not match topology (1K4C_clean.top, 216)<br>
-------------------------------------------------------<br>
<br>
I don't know where I have done the mistake...your help will<br>
be highly<br>
appreciable in this case.<br>
<br>
<br>
Here you've got a 7-atom difference, and...<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<br>
(1K4C_cg.gro, 1127)<br>
does not match topology<br>
(1K4C.top, 1166)<br>
-------------------------------------------------------<br>
<br>
<br>
...here you're different by 39 atoms. That indicates a procedure<br>
that differed by more than just not adding solvent.<br>
<br>
With a complex multi-step system preparation, you are much<br>
better served by writing the steps down in a shell script so<br>
that you really do things the same way every time. Science is<br>
still science, even on a computer, and your work must be<br>
reproducible. Moreover, then when you ask for help, you're not<br>
presenting contradictions and non sequiturs that frustrate<br>
attempts to help you :-)<br>
<br>
In any case, my earlier advice still applies - it should be a<br>
matter of 10 minutes work to compare your clean .itp and .gro to<br>
see what atoms are causing the problem. Then, work backwards.<br>
<br>
Mark<br>
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<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>
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<br>
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</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>
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