Francesco Pietra wrote:
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Francesco Pietra wrote:
grep W solvated.gro | wc -l
and use that number in the topology?
I forgot to add that the graphic program uses the above grep command,
I don't understand this statement.
giving the same number of W as the line command. The number of DCCP is
diminished by those deleted in inserting the protein, but the grompp
command complains that .gro does not matches .top. If no further water
is added graphically, everything works.
This is where exact commands (in sequence) really help, or at least a
stepwise procedure. Are you adding a protein into a box that contains
DCCP+water, or are you inserting the protein into DCCP, then adding water?
What is the exact error that grompp is giving you? That the number of
coordinates don't match? atom names don't match?
What I did follows. I am using the actual filenames and page numbers
for my reference.
(1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4).
(2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4).
(3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4).
(4) inserting the pore region of the cg protein into the bilayer in
the obvious orientation, then removing all dppc superimposed to the
protein plus an extra margin of 10A, to get mod21.aligned.pdb and
dppc.aligned.pdb (according to as described for all-atoms in the paper
I referred to in this thread) (p. 4)
(5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o
mod21+dccp.box.pdb
resulted in the protein at a corner of the cubic box. This is probably
because I was using a homology model, i.e., there was no CRYSTAL
record. It was nonetheless surprising because the two .pdb files to
combine had the same box size (p. 5).
Box manipulation can be tricky. I would recommend doing the alignment with
editconf, for example, to place the bilayer and protein centers at the center of
the box, you would issue:
editconf -f mod21.aligned.pdb -o mod21.aligned.center.pdb -c -box 11 -bt cubic
And analogously for the bilayer. If the center must be shifted relative to the
box center, you can supply to exact coordinates with editconf -center.
(6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb
resulted in a correct insertion of the pore region into the bilayer,
the latter correctly oriented. Filename dppc+mod21.pdb (p. 6).
The bilayer originally was made of 128 dppc and 2000 W. After
insertion of the protein, the system was 1 multimeric protein, 85 dppc
and 1767 W (taking into account that there are 12 atoms per dppc).
(7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o
dppc+mod21+W.box.pdb
resulted in the protein at a corner of the solvating box, which only
comprised the pore region inserted into the bilayer. I.e., the large
non-pore region of the protein was not solvated. On making the box
bigger and bigger also the non-pore region was solvated but the pore
region exited the bilayer and entered the water region. Which
situation could not be accepted (pp. 8-9).
I think genbox is inducing this effect because it is trying to assemble your
system within the -box you have defined. I am not aware of any known issues
with using genbox -box, but as a matter of routine, I always define the box with
editconf prior to running genbox. Again, I don't know of anything that is
broken about genbox, but it would be worthwhile to eliminate this as a potential
problem.
I was unable to detect whether I was using wrong commands with genbox,
and therefore I abandoned genbox.
(8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the
non-pore region of the protein-dppc ensemble by adding a preformed box
of water (that is, using the methodology of step 4). Thus,
dppc+mod21.pd was aligned with a water box of 5400 W, removing all W
superimposed to the non-pore region of mod21+dppc, plus a margin of
10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD
(or as corresponding .pdb file in CHIMERA), that is, the non-pore
region is solvated (pp. 11-12).
In my hands, the .pdb file describing this ensemble did not allow to
generate a .tpr file. The ensemble was made of
Protein 1 (multimeric)
DPPC 85
W 6008
which data were used for the .top file. Command
$ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr
resulted in error: number of coordinates in coordinate file
(dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top,
9903) (p. 19).
Can you post the first and last few lines of dppc+mod21+W.gro (i.e., "head
dppc+mod21+W.gro" and "tail dppc+mod21+W.gro")?
-Justin
(9) Starting directly from dppc+mod21.pdb (from step 6), commad
$ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro
5662 atoms in 3122 residues
Volume: 1700 nm^3
Density: 99.5996
SOL: 0
followed by command
$ grompp -f minimize.mdp -c dppc+mod21.gro -p dppc+mod21.top -o minimize.tpr
where, for the .top file,
[molecule]
Protein 1
DPPC 85
W 1767 (derived as indicated at step 6)
generated correctly the .tpr file (p. 20).
.......................
I hope to have illustrated in sufficient details the procedure so as
my mistakes could be detected.
thanks for help
francesco
-Justin
--
========================================
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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--
========================================
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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