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 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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