Thanks for your reply.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: 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, 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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