[gmx-users] grompp in KALP15-DPPC

[Shima Arasteh]

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? 

 
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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