Dear Gromacs Users,<br><br>While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have some queries regarding the INFLATEGRO, Please have patience to read and answer my queries:<br><br>1) does the system.gro should include the position restrained file of <font face="Arial"><font size="3"><font face="courier" size="-1">KALP_newbox.gro</font></font></font> after running <font face="Arial"><font size="3"><font face="courier" size="-1">genrestr, as i combined the ouput of genestr to </font></font></font><font face="Arial"><font size="3"><font face="courier" size="-1">dppc128.gro to generate system.gro.<br>
<br>2) should both the box vectors in system.gro to be deleted or just the ones under KALP structure, the other being at the end of the file.<br><br>3)then I updated the system.gro file to 17503 atoms from 138 atoms and executed this command: perl INFLATEGRO system.gro 4 DPP 14 inflated_system.gro 5 areaperlipid.dat<br>
<br>the output was as under:<br>Reading..... <br>Scaling lipids....<br>There are 128 lipids...<br>with 50 atoms per lipid..<br><br>Determining upper and lower leaflet...<br>64 lipids in the upper...<br>64 lipids in the lower leaflet <br>
<br>Centering protein....<br>Checking for overlap....<br>...this might actually take a while....<br>100 % done...<br>There are 2 lipids within cut-off range...<br>1 will be removed from the upper leaflet...<br>1 will be removed from the lower leaflet...<br>
<br>Writing scaled bilayer & centered protein...<br><br><br>Calculating Area per lipid...<br>Protein X-min/max: 26 40<br>Protein Y-min/max: 25 39<br>X-range: 14 A Y-range: 14 A<br>Building 14 X 14 2D grid on protein coordinates...<br>
Calculating area occupied by protein..<br>full TMD..<br>upper TMD....<br>lower TMD....<br>Area per protein: 2 nm^2<br>Area per lipid: 10.4716089904762 nm^2<br><br>Area per protein, upper half: 1.75 nm^2<br>Area per lipid, upper leaflet : 10.4755772444444 nm^2<br>
<br>Area per protein, lower half: 2 nm^2<br>Area per lipid, lower leaflet : 10.4716089904762 nm^2<br><br>Writing Area per lipid...<br>Done!<br><br>then, i updated the topol_dppc_top to 126 lipids<br><br>; System specifications<br>
[ system ]<br>126-Lipid DPPC Bilayer <br><br>[ molecules ]<br>; molecule name nr.<br>DPPC 126<br>SOL 3655<br><br>and also updated the number of atoms in system.gro to 17403 and added 126 DPPC and 3655 SOL to topol.top file and executed the grompp command for minimization as under:<br>
<br>grompp -f minim.mdp </font></font></font><font face="Arial"><font size="3"><font face="courier" size="-1">-c system.gro -p topol.top -o em.tpr<br><br>minim.mdp parameters are as under:<br>; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>define = -DSTRONG_POSRES<br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>rlist = 1.2 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.2 ; Short-range electrostatic cut-off<br>rvdw = 1.2 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br>the ouput of grompp was :<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>
Generated 813 of the 2346 non-bonded parameter combinations<br><br>ERROR 1 [file topol.top, line 535]:<br> No default G96Angle types<br><br>Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp<br>
Excluding 3 bonded neighbours molecule type 'Protein'<br>Excluding 3 bonded neighbours molecule type 'DPPC'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>NOTE 1 [file topol.top, line 904]:<br>
System has non-zero total charge: 4.000011e+00<br> <br><br><br>processing coordinates...<br><br>WARNING 1 [file topol.top, line 904]:<br> Bad box in file system.gro<br><br>Generated a cubic box 6.612 x 6.639 x 6.741<br>
Warning: atom name 6439 in topol.top and system.gro does not match (OW - C1)<br>Warning: atom name 6440 in topol.top and system.gro does not match (HW1 - C2)<br>Warning: atom name 6441 in topol.top and system.gro does not match (HW2 - C3)<br>
Warning: atom name 6442 in topol.top and system.gro does not match (OW - N4)<br>Warning: atom name 6443 in topol.top and system.gro does not match (HW1 - C5)<br>Warning: atom name 6444 in topol.top and system.gro does not match (HW2 - C6)<br>
Warning: atom name 6445 in topol.top and system.gro does not match (OW - O7)<br>Warning: atom name 6446 in topol.top and system.gro does not match (HW1 - P8)<br>Warning: atom name 6447 in topol.top and system.gro does not match (HW2 - O9)<br>
Warning: atom name 6448 in topol.top and system.gro does not match (OW - O10)<br>Warning: atom name 6449 in topol.top and system.gro does not match (HW1 - O11)<br>Warning: atom name 6450 in topol.top and system.gro does not match (HW2 - C12)<br>
Warning: atom name 6451 in topol.top and system.gro does not match (OW - C13)<br>Warning: atom name 6452 in topol.top and system.gro does not match (HW1 - O14)<br>Warning: atom name 6453 in topol.top and system.gro does not match (HW2 - C15)<br>
Warning: atom name 6454 in topol.top and system.gro does not match (OW - O16)<br>Warning: atom name 6455 in topol.top and system.gro does not match (HW1 - C17)<br>Warning: atom name 6456 in topol.top and system.gro does not match (HW2 - C18)<br>
Warning: atom name 6457 in topol.top and system.gro does not match (OW - C19)<br>Warning: atom name 6458 in topol.top and system.gro does not match (HW1 - C20)<br>(more than 20 non-matching atom names)<br><br>WARNING 2 [file topol.top, line 904]:<br>
10965 non-matching atom names<br> atom names from topol.top will be used<br> atom names from system.gro will be ignored<br><br><br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br>
<br>There was 1 note<br><br>There were 2 warnings<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.3<br>Source code file: grompp.c, line: 986<br><br>Fatal error:<br>There was 1 error in input file(s)<br>
-------------------------------------------------------<br><br>then I executed </font></font></font><font face="Arial"><font size="3"><font face="courier" size="-1"><font face="courier" size="-1">mdrun -v -deffnm em</font></font></font></font><font size="-1"><font face="courier"><br>
<br>the output is :<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 50000<br>Step= 0, Dmax= 1.0e-02 nm, Epot= -3.06213e+05 Fmax= 5.37269e+03, atom= 3275<br>Step= 1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax= 2.40667e+03, atom= 3024<br>
Step= 3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05 Fmax= 2.89119e+03, atom= 4225<br>Step= 5, Dmax= 3.6e-03 nm, Epot= -3.12590e+05 Fmax= 1.46759e+03, atom= 1365<br>Step= 6, Dmax= 4.3e-03 nm, Epot= -3.13033e+05 Fmax= 3.84000e+03, atom= 1365<br>
Step= 7, Dmax= 5.2e-03 nm, Epot= -3.13600e+05 Fmax= 2.88681e+03, atom= 1365<br>Step= 8, Dmax= 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93217e+03, atom= 1365<br>Step= 9, Dmax= 7.5e-03 nm, Epot= -3.14102e+05 Fmax= 4.72470e+03, atom= 1365<br>
Step= 11, Dmax= 4.5e-03 nm, Epot= -3.14801e+05 Fmax= 9.91096e+02, atom= 1365<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to Fmax < 1000 in 12 steps<br>Potential Energy = -3.1480106e+05<br>
Maximum force = 9.9109589e+02 on atom 1365<br>Norm of force = 1.2181871e+02<br> <br>so, as the minimization was occuring i started compressing the box using this command : perl INFLATEGRO system.gro 0.95 DPP 0 inflated_system.gro 5 areaperlipid.dat<br>
<br>the ouput was as follows:<br>Reading..... <br>Scaling lipids....<br>There are 128 lipids...<br>with 50 atoms per lipid..<br><br>Determining upper and lower leaflet...<br>64 lipids in the upper...<br>64 lipids in the lower leaflet <br>
<br>Centering protein....<br>Writing scaled bilayer & centered protein...<br><br><br>Calculating Area per lipid...<br>Protein X-min/max: 26 40<br>Protein Y-min/max: 25 39<br>X-range: 14 A Y-range: 14 A<br>Building 14 X 14 2D grid on protein coordinates...<br>
Calculating area occupied by protein..<br>full TMD..<br>upper TMD....<br>lower TMD....<br>Area per protein: 2 nm^2<br>Area per lipid: 0.551947761890625 nm^2<br><br>Area per protein, upper half: 1.75 nm^2<br>Area per lipid, upper leaflet : 0.555854011890625 nm^2<br>
<br>Area per protein, lower half: 2 nm^2<br>Area per lipid, lower leaflet : 0.551947761890625 nm^2<br><br>Writing Area per lipid...<br>Done!<br><br>finally i repeated the mdrun -v -deffnm em and perl INFLATEGRO system.gro 0.95 DPP 0 inflated_system.gro 5 areaperlipid.dat 27 times but there was no change in the area per lipid values.<br>
<br>Could any body help me whether I am following the tutorial correctly, and if not please correct me by your suggestions<br><br>Ram<br><br></font></font><font face="Arial"><font size="3"><font face="courier" size="-1"><br>
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