sunny mishra wrote:
Hi Mark and Justin,
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.
I got the 1K4C_cleanCG.seq file using grep command like this
grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq
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.
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....
seq2itp.pl 1K4C_cleanCG.seq 1K4C_clean.ssd > 1K4C_cleanCG.itp
OR
seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp
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.
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.
-Justin
Thanks,
Sunny
On Wed, Aug 19, 2009 at 6:54 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
In addition to everything Mark said, also realize that there may be
a fundamental problem in everything you are doing: there are missing
atoms in the original 1K4C structure. If you have not modeled them
back in, the appropriate CG particles will not necessarily all be
placed in your CG structure, but the topology will be written such
that it expects all the correct atoms to be there.
At first glance, Arg117 is going to cause headaches - it is missing
all atoms beyond CB, and since CG and NE are necessary for MARTINI's
definition of an ARG residue, you can bet this will be a problem.
-Justin
Mark Abraham wrote:
sunny mishra wrote:
Hi Justin,
Thanks for the reply and here is the following which I am
doing. I would
appreciate if you can point out my errors.
1) I am working on 1K4C (KcSA) and i downloaded that from
www.pdb.org <http://www.pdb.org> 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.
2) After getting the 1K4C_clean.pdb I converted the atomic
structure to CG
structure using awk script...something like this
awk -f atom2cg.awk 1K4C_clean.pdb > 1K4C_cleanCG.pdb
Here you create 1K4C_cleanCG.pdb
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...
But below you create your .itp starting from "1K4C_clean", which
at least means you haven't copied your correct grep line, and
might indicate the mismatch between your structure and topology.
grep -A 1 1K4C_clean 1K4C_clean.txt > 1K4C_clean.seq
4) Then using dssp I got the .ssd file for 1K4C_clean.pdb....
dsspcmbi 1K4C_clean.pdb 1K4C_clean.dssp
dssp2ssd.py 1K4C_clean.dssp -o 1K4C_clean.ssd
5) After preparing the secondary structure files I generated
the MARTINI
topology files like this :
seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp
6) The next step is to make the topology file and I made
like this.....
; Include Martini Topology
#include "martini_v2.1.itp"
; Include protein topology
#include "1K4C_clean.itp"
[ system ]
; Name
Membrane Protein
[ molecules ]
; compound #mols
Protein 1
7) Then I made the .gro file using genbox.....
genbox -cp 1K4C_cleanCG.pdb -box 10 10 10 -o 1K4C_cleanCG.gro
(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)
A .gro file is almost never essential. A structure file with a
suitable periodic box can be.
8) Now I want to minimize the system.....
grompp -f em.mdp -c 1K4C_cleanCG.gro -p 1K4C_clean.top
-maxwarn 10
and then error comes...........
:-) G R O M A C S
(-:
GROningen MAchine for Chemical Simulation
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk
Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
Copyright (c) 2001-2008, The GROMACS development
team,
check out http://www.gromacs.org for more
information.
This program is free software; you can redistribute
it and/or
modify it under the terms of the GNU General Public
License
as published by the Free Software Foundation; either
version 2
of the License, or (at your option) any later
version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file with MD
parameters
-po mdout.mdp Output grompp input file with MD
parameters
-c 1K4C_cleanCG.pdb Input Structure file: gro g96
pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb
tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96
pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1K4C_clean.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory:
trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after
this time.
-[no]rmvsbds bool yes Remove constant bonded
interactions with virtual
sites
-maxwarn int 10 Number of allowed warnings
during input
processing
-[no]zero bool no Set parameters for bonded
interactions
without
defaults to zero instead of
generating an
error
-[no]renum bool yes Renumber atomtypes and minimize
number
of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
checking input for internal consistency...
NOTE 1 [file em.mdp, line unknown]:
For energy conservation with switch/shift potentials, rlist
should be 0.1
to 0.3 nm larger than rcoulomb.
NOTE 2 [file em.mdp, line unknown]:
For energy conservation with switch/shift potentials, rlist
should be 0.1
to 0.3 nm larger than rvdw.
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
NOTE 3 [file 1K4C_clean.top, line 15]:
System has non-zero total charge: 2.000000e+00
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (1K4C_cleanCG.pdb, 209)
does not match topology (1K4C_clean.top, 216)
-------------------------------------------------------
I don't know where I have done the mistake...your help will
be highly
appreciable in this case.
Here you've got a 7-atom difference, and...
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file
(1K4C_cg.gro, 1127)
does not match topology
(1K4C.top, 1166)
-------------------------------------------------------
...here you're different by 39 atoms. That indicates a procedure
that differed by more than just not adding solvent.
With a complex multi-step system preparation, you are much
better served by writing the steps down in a shell script so
that you really do things the same way every time. Science is
still science, even on a computer, and your work must be
reproducible. Moreover, then when you ask for help, you're not
presenting contradictions and non sequiturs that frustrate
attempts to help you :-)
In any case, my earlier advice still applies - it should be a
matter of 10 minutes work to compare your clean .itp and .gro to
see what atoms are causing the problem. Then, work backwards.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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