Hi Justin and Mark,
I just realized that I have some missing atoms in my .gro file when I
compared with .itp file and may be this is causing the problem. The
atoms which are missing what should I do with them. Should I delete both
from .itp and .gro file OR do i have to add in my .gro file and if I
have to add them then how?
for example in my .itp file there are 2 ILE but in my .gro file there is
only 1 ILE. So should i add another ILE in my .gro file or delete 2 ILE
from .itp and 1ILE from .gro. Thanks in advance.
Sunny
On Wed, Aug 19, 2009 at 7:23 PM, sunny mishra <[email protected]
<mailto:[email protected]>> wrote:
Alright. Sounds good to me. let me check that out and i will let you
know the progress.
Thanks,
Sunny
On Wed, Aug 19, 2009 at 7:19 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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]>
<mailto:[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>
<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> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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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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