[gmx-users] grompp in KALP15-DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Aug 25 18:50:21 CEST 2012

 Thanks for your reply.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, August 25, 2012 9:16 PM
Subject: Re: [gmx-users] grompp in KALP15-DPPC

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, 

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.


> Sincerely, Shima
> ----- Original Message ----- From: Justin Lemkul <jalemkul at vt.edu> To: Shima
> Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at 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

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