On 8/25/12 12:41 PM, Shima Arasteh wrote:
The number of DPPC molecules were 126. I changed it to 128 in topol.top, then
the grompp didn't give me any fatal error. I had changed the number of DPPC
in top file in last step when the inflateGRO reporst that 2 DPPC were
removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible?
Not in the least. You should make one change to the [molecules] (when
InflateGRO deletes lipids) and never manually adjust it again. You need to
check your work, because I suspect you're using the wrong files (either topology
or coordinates) because suddenly there's a mismatch that shouldn't be happening.
You can always check what's in your coordinate file with grep to do counting,
e.g.:
grep -c P8 (name of your coordinate file)
That will tell you the number of DPPC lipids. Likewise, you can count water
molecules (another common source of error) with:
grep -c OW (name of your coordinate file)
If your coordinate file somehow has 128 DPPC again, then you're using the wrong
file. Once deleted, they don't get added back.
-Justin
Sincerely, Shima
----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima
Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org> Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject:
Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12 12:26 PM, Shima Arasteh wrote:
Hi, I am doing the simulation of KALP15 in DPPC following the Justin's
tutorial.
For the step of solvation I ran this command: # genbox -cp system.gro -cs
spc216.gro -o system_solv.gro -p topol.top
The output of this step is as here: Reading solute configuration frame t=
1.000 Containing 17503 atoms in 3800 residues Initialising van der waals
distances...
WARNING: masses and atomic (Van der Waals) radii will be determined based
on residue and atom names. These numbers can deviate from the correct mass
and radius of the atom type.
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances... Will generate new solvent
configuration of 4x4x4 boxes Generating configuration Sorting
configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues
Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were
outside the box Neighborsearching with a cut-off of 1.125 Table routines
are used for coulomb: FALSE Table routines are used for vdw: FALSE
Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge:
0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri =
152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927
pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610
pairs, removed 60 atoms. Added 252 molecules Generated solvent containing
756 atoms in 252 residues Writing generated configuration to
system_solv.gro
Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame
t= 1.000
Output configuration contains 18259 atoms in 4052 residues Volume
: 272.811 (nm^3) Density : 947.87 (g/l) Number of
SOL molecules: 3907
Processing topology Removing line #929 'SOL 533' from
topology file (topol.top)
Then running grompp for the next step ( neutralization )
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
But the error is:
Fatal error: number of coordinates in coordinate file (system_solv.gro,
18259) does not match topology (topol.top, 18159) For more information and
tips for troubleshooting, please check the GROMACS
Would you pleas help me? Do I need to modify the .top file before running
grompp?
Well, something doesn't match, so yes. But at the same time, if you're
properly maintained the topology thus far, then you shouldn't have to. A
difference of 100 atoms suggests there are 2 extra DPPC molecules in the
coordinate file relative to the topology. I have no idea how you would have
produced such a mismatch though.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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