[gmx-users] lipid itp file problem

[Justin A. Lemkul]

I don't know about anybody else, but all I see is one continuous block 
of text.  Please format your emails as plain text and ensure that your 
copying/pasting of parameters/.mdp files is appropriate.

That said, I also highly doubt that anyone is going to go through your 
PRODRG-generated topology searching for errors.  If you drew/entered the 
molecule correctly in PRODRG, all the bonds should be there. 

Try to work things scientifically: minimize the bilayer first, in the 
absence of any protein/drug/whatever else you add to see if that truly 
is the problem.  Membrane protein systems are complicated, and the 
initial minimization and equilibration steps are very sensitive to how 
you set up the system (insertion of protein, addition of water/other 
molecules).

-Justin

serdar durdagi wrote:
> Dear all, I am trying to simulate drug at the binding site of the 
> receptor surrounded by DPPC bilayer system. I have problem at the 
> energy minimisation step. Always, I am getting below error message: 
> Back Off! I just backed up last.edr to ./#last.edr.8# Steepest 
> Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 500 
> Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which 
> is larger than the 1-4 table size 1.000 nm These are ignored for the 
> rest of the simulation This usually means your system is exploding, if 
> not, you should increase table-extension in your mdp file Step= 0, 
> Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 2662 
> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, atom= 
> 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 8.84756e+11, 
> atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 Fmax= 
> 5.31692e+10, atom= 2661 Step= 4, Dmax= 1.7e-02 nm, Epot= 5.09105e+08 
> Fmax= 2.70368e+09, atom= 3603 Step= 5, Dmax= 2.1e-02 nm, Epot= 
> 3.53172e+08 Fmax= 4.50870e+08, atom= 2661 .... When I try to increase 
> table-extension to more than 1.0, 1-4 interaction always increases. I 
> checked the *.gro file, it seems during the minimisation, bonds at 
> protein and drg molecules are fine however, bonds at the DPPC 
> molecules are broken. I guess problem is at the *.itp file of dppc. I 
> produced *.itp file of DPPC from PRODRG. *itp file of lipid and *.mdp 
> file for energy minimisation are attached below. Could any body give a 
> clue for the solution? Many thanks in advanced. Serdar Durdagi LIPID 
> ITP FILE: [ moleculetype ] ; Name nrexcl MOL 3 [ atoms ] ; nr type 
> resnr resid atom cgnr charge mass 1 CH3 1 MOL C8 1 -0.033 15.0350 2 
> CH2 1 MOL C1 1 0.008 14.0270 3 CH2 1 MOL C45 1 0.008 14.0270 4 CH2 1 
> MOL C44 1 0.009 14.0270 5 CH2 1 MOL C43 1 0.008 14.0270 6 CH2 1 MOL 
> C42 2 0.000 14.0270 7 CH2 1 MOL C41 2 0.000 14.0270 8 CH2 1 MOL C40 3 
> 0.000 14.0270 9 CH2 1 MOL C39 3 0.000 14.0270 10 CH2 1 MOL C38 4 0.000 
> 14.0270 11 CH2 1 MOL C37 4 0.000 14.0270 12 CH2 1 MOL C36 5 0.000 
> 14.0270 13 CH2 1 MOL C35 5 0.000 14.0270 14 CH2 1 MOL C34 6 0.000 
> 14.0270 15 CH2 1 MOL C33 7 0.036 14.0270 16 C 1 MOL C32 7 0.438 
> 12.0110 17 O 1 MOL O46 7 -0.551 15.9994 18 OS 1 MOL O31 7 -0.160 
> 15.9994 19 CS1 1 MOL C13 7 0.237 13.0190 20 CH2 1 MOL C12 8 0.000 
> 14.0270 21 OS 1 MOL O11 9 -0.256 15.9994 22 P 1 MOL P8 9 0.998 30.9738 
> 23 OM 1 MOL O10 9 -0.743 15.9994 24 OM 1 MOL O9 9 -0.743 15.9994 25 OS 
> 1 MOL O4 9 -0.256 15.9994 26 CH2 1 MOL C3 10 0.041 14.0270 27 CH2 1 
> MOL C2 10 0.041 14.0270 28 NL 1 MOL N1 10 0.918 14.0067 29 CH3 1 MOL 
> C6 11 0.000 15.0350 30 CH3 1 MOL C5 11 0.000 15.0350 31 CH3 1 MOL C7 
> 12 0.000 15.0350 32 CS2 1 MOL C14 13 0.242 14.0270 33 OS 1 MOL O15 13 
> -0.162 15.9994 34 C 1 MOL C16 13 0.437 12.0110 35 O 1 MOL O30 13 
> -0.553 15.9994 36 CH2 1 MOL C17 13 0.036 14.0270 37 CH2 1 MOL C18 14 
> 0.000 14.0270 38 CH2 1 MOL C19 14 0.000 14.0270 39 CH2 1 MOL C20 15 
> 0.000 14.0270 40 CH2 1 MOL C21 15 0.000 14.0270 41 CH2 1 MOL C22 16 
> 0.000 14.0270 42 CH2 1 MOL C23 16 0.000 14.0270 43 CH2 1 MOL C24 17 
> 0.000 14.0270 44 CH2 1 MOL C25 17 0.000 14.0270 45 CH2 1 MOL C26 18 
> 0.000 14.0270 46 CH2 1 MOL C27 19 0.008 14.0270 47 CH2 1 MOL C28 19 
> 0.008 14.0270 48 CH2 1 MOL C29 19 0.008 14.0270 49 CH2 1 MOL C9 19 
> 0.009 14.0270 50 CH3 1 MOL C10 19 -0.033 15.0350 [ bonds ] ; ai aj fu 
> c0, c1, ... 1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1 2 3 1 0.153 
> 334720.0 0.153 334720.0 ; C1 C45 3 4 1 0.153 334720.0 0.153 334720.0 ; 
> C45 C44 4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43 5 6 1 0.153 
> 334720.0 0.153 334720.0 ; C43 C42 6 7 1 0.153 334720.0 0.153 334720.0 
> ; C42 C41 7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40 8 9 1 0.153 
> 334720.0 0.153 334720.0 ; C40 C39 9 10 1 0.153 334720.0 0.153 334720.0 
> ; C39 C38 10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37 11 12 1 
> 0.153 334720.0 0.153 334720.0 ; C37 C36 12 13 1 0.153 334720.0 0.153 
> 334720.0 ; C36 C35 13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34 14 
> 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33 15 16 1 0.153 334720.0 
> 0.153 334720.0 ; C33 C32 16 17 1 0.123 502080.0 0.123 502080.0 ; C32 
> O46 16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31 18 19 1 0.144 
> 251040.0 0.144 251040.0 ; O31 C13 19 20 1 0.153 251040.0 0.153 
> 251040.0 ; C13 C12 19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14 20 
> 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11 21 22 1 0.161 251040.0 
> 0.161 251040.0 ; O11 P8 22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10 
> 22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9 22 25 1 0.161 251040.0 
> 0.161 251040.0 ; P8 O4 25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3 
> 26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2 27 28 1 0.147 376560.0 
> 0.147 376560.0 ; C2 N1 28 29 1 0.147 376560.0 0.147 376560.0 ; N1 C6 
> 28 30 1 0.147 376560.0 0.147 376560.0 ; N1 C5 28 31 1 0.147 376560.0 
> 0.147 376560.0 ; N1 C7 32 33 1 0.144 251040.0 0.144 251040.0 ; C14 O15 
> 33 34 1 0.136 376560.0 0.136 376560.0 ; O15 C16 34 35 1 0.123 502080.0 
> 0.123 502080.0 ; C16 O30 34 36 1 0.153 334720.0 0.153 334720.0 ; C16 
> C17 36 37 1 0.153 334720.0 0.153 334720.0 ; C17 C18 37 38 1 0.153 
> 334720.0 0.153 334720.0 ; C18 C19 38 39 1 0.153 334720.0 0.153 
> 334720.0 ; C19 C20 39 40 1 0.153 334720.0 0.153 334720.0 ; C20 C21 40 
> 41 1 0.153 334720.0 0.153 334720.0 ; C21 C22 41 42 1 0.153 334720.0 
> 0.153 334720.0 ; C22 C23 42 43 1 0.153 334720.0 0.153 334720.0 ; C23 
> C24 43 44 1 0.153 334720.0 0.153 334720.0 ; C24 C25 44 45 1 0.153 
> 334720.0 0.153 334720.0 ; C25 C26 45 46 1 0.153 334720.0 0.153 
> 334720.0 ; C26 C27 46 47 1 0.153 334720.0 0.153 334720.0 ; C27 C28 47 
> 48 1 0.153 334720.0 0.153 334720.0 ; C28 C29 48 49 1 0.153 334720.0 
> 0.153 334720.0 ; C29 C9 49 50 1 0.153 334720.0 0.153 334720.0 ; C9 C10 
> [ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; C8 C44 2 5 1 ; C1 C43 3 6 1 ; 
> C45 C42 4 7 1 ; C44 C41 5 8 1 ; C43 C40 6 9 1 ; C42 C39 7 10 1 ; C41 
> C38 8 11 1 ; C40 C37 9 12 1 ; C39 C36 10 13 1 ; C38 C35 11 14 1 ; C37 
> C34 12 15 1 ; C36 C33 13 16 1 ; C35 C32 14 17 1 ; C34 O46 14 18 1 ; 
> C34 O31 15 19 1 ; C33 C13 16 20 1 ; C32 C12 16 32 1 ; C32 C14 17 19 1 
> ; O46 C13 18 21 1 ; O31 O11 18 33 1 ; O31 O15 19 22 1 ; C13 P8 19 34 1 
> ; C13 C16 20 23 1 ; C12 O10 20 24 1 ; C12 O9 20 25 1 ; C12 O4 20 33 1 
> ; C12 O15 21 26 1 ; O11 C3 21 32 1 ; O11 C14 22 27 1 ; P8 C2 23 26 1 ; 
> O10 C3 24 26 1 ; O9 C3 25 28 1 ; O4 N1 26 29 1 ; C3 C6 26 30 1 ; C3 C5 
> 26 31 1 ; C3 C7 32 35 1 ; C14 O30 32 36 1 ; C14 C17 33 37 1 ; O15 C18 
> 34 38 1 ; C16 C19 35 37 1 ; O30 C18 36 39 1 ; C17 C20 37 40 1 ; C18 
> C21 38 41 1 ; C19 C22 39 42 1 ; C20 C23 40 43 1 ; C21 C24 41 44 1 ; 
> C22 C25 42 45 1 ; C23 C26 43 46 1 ; C24 C27 44 47 1 ; C25 C28 45 48 1 
> ; C26 C29 46 49 1 ; C27 C9 47 50 1 ; C28 C10 [ angles ] ; ai aj ak fu 
> c0, c1, ... 1 2 3 1 111.0 460.2 111.0 460.2 ; C8 C1 C45 2 3 4 1 111.0 
> 460.2 111.0 460.2 ; C1 C45 C44 3 4 5 1 111.0 460.2 111.0 460.2 ; C45 
> C44 C43 4 5 6 1 111.0 460.2 111.0 460.2 ; C44 C43 C42 5 6 7 1 111.0 
> 460.2 111.0 460.2 ; C43 C42 C41 6 7 8 1 111.0 460.2 111.0 460.2 ; C42 
> C41 C40 7 8 9 1 111.0 460.2 111.0 460.2 ; C41 C40 C39 8 9 10 1 111.0 
> 460.2 111.0 460.2 ; C40 C39 C38 9 10 11 1 111.0 460.2 111.0 460.2 ; 
> C39 C38 C37 10 11 12 1 111.0 460.2 111.0 460.2 ; C38 C37 C36 11 12 13 
> 1 111.0 460.2 111.0 460.2 ; C37 C36 C35 12 13 14 1 111.0 460.2 111.0 
> 460.2 ; C36 C35 C34 13 14 15 1 111.0 460.2 111.0 460.2 ; C35 C34 C33 
> 14 15 16 1 111.0 460.2 111.0 460.2 ; C34 C33 C32 15 16 17 1 121.0 
> 502.1 121.0 502.1 ; C33 C32 O46 15 16 18 1 120.0 418.4 120.0 418.4 ; 
> C33 C32 O31 17 16 18 1 120.0 418.4 120.0 418.4 ; O46 C32 O31 16 18 19 
> 1 109.5 334.7 109.5 334.7 ; C32 O31 C13 18 19 20 1 109.5 284.5 109.5 
> 284.5 ; O31 C13 C12 18 19 32 1 109.5 284.5 109.5 284.5 ; O31 C13 C14 
> 20 19 32 1 109.5 251.0 109.5 251.0 ; C12 C13 C14 19 20 21 1 111.0 
> 460.2 111.0 460.2 ; C13 C12 O11 20 21 22 1 120.0 397.5 120.0 397.5 ; 
> C12 O11 P8 21 22 23 1 109.6 397.5 109.6 397.5 ; O11 P8 O10 21 22 24 1 
> 109.6 397.5 109.6 397.5 ; O11 P8 O9 21 22 25 1 103.0 397.5 103.0 397.5 
> ; O11 P8 O4 23 22 24 1 120.0 585.8 120.0 585.8 ; O10 P8 O9 23 22 25 1 
> 109.6 397.5 109.6 397.5 ; O10 P8 O4 24 22 25 1 109.6 397.5 109.6 397.5 
> ; O9 P8 O4 22 25 26 1 120.0 397.5 120.0 397.5 ; P8 O4 C3 25 26 27 1 
> 109.5 460.2 109.5 460.2 ; O4 C3 C2 26 27 28 1 109.5 460.2 109.5 460.2 
> ; C3 C2 N1 27 28 29 1 109.5 376.6 109.5 376.6 ; C2 N1 C6 27 28 30 1 
> 109.5 376.6 109.5 376.6 ; C2 N1 C5 27 28 31 1 109.5 376.6 109.5 376.6 
> ; C2 N1 C7 29 28 30 1 109.5 376.6 109.5 376.6 ; C6 N1 C5 29 28 31 1 
> 109.5 376.6 109.5 376.6 ; C6 N1 C7 30 28 31 1 109.5 376.6 109.5 376.6 
> ; C5 N1 C7 19 32 33 1 109.5 284.5 109.5 284.5 ; C13 C14 O15 32 33 34 1 
> 109.5 334.7 109.5 334.7 ; C14 O15 C16 33 34 35 1 120.0 418.4 120.0 
> 418.4 ; O15 C16 O30 33 34 36 1 120.0 418.4 120.0 418.4 ; O15 C16 C17 
> 35 34 36 1 121.0 502.1 121.0 502.1 ; O30 C16 C17 34 36 37 1 111.0 
> 460.2 111.0 460.2 ; C16 C17 C18 36 37 38 1 111.0 460.2 111.0 460.2 ; 
> C17 C18 C19 37 38 39 1 111.0 460.2 111.0 460.2 ; C18 C19 C20 38 39 40 
> 1 111.0 460.2 111.0 460.2 ; C19 C20 C21 39 40 41 1 111.0 460.2 111.0 
> 460.2 ; C20 C21 C22 40 41 42 1 111.0 460.2 111.0 460.2 ; C21 C22 C23 
> 41 42 43 1 111.0 460.2 111.0 460.2 ; C22 C23 C24 42 43 44 1 111.0 
> 460.2 111.0 460.2 ; C23 C24 C25 43 44 45 1 111.0 460.2 111.0 460.2 ; 
> C24 C25 C26 44 45 46 1 111.0 460.2 111.0 460.2 ; C25 C26 C27 45 46 47 
> 1 111.0 460.2 111.0 460.2 ; C26 C27 C28 46 47 48 1 111.0 460.2 111.0 
> 460.2 ; C27 C28 C29 47 48 49 1 111.0 460.2 111.0 460.2 ; C28 C29 C9 48 
> 49 50 1 111.0 460.2 111.0 460.2 ; C29 C9 C10 [ dihedrals ] ; ai aj ak 
> al fu c0, c1, m, ... 16 15 18 17 2 0.0 1673.6 0.0 1673.6 ; imp C32 C33 
> O31 O46 34 33 36 35 2 0.0 1673.6 0.0 1673.6 ; imp C16 O15 C17 O30 19 
> 18 32 20 2 35.3 836.8 35.3 836.8 ; imp C13 O31 C14 C12 22 21 24 23 2 
> 35.3 836.8 35.3 836.8 ; imp P8 O11 O9 O10 28 27 29 30 2 35.3 836.8 
> 35.3 836.8 ; imp N1 C2 C6 C5 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C44 
> C45 C1 C8 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C43 C44 C45 C1 6 5 4 3 1 
> 0.0 5.9 3 0.0 5.9 3 ; dih C42 C43 C44 C45 7 6 5 4 1 0.0 5.9 3 0.0 5.9 
> 3 ; dih C41 C42 C43 C44 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C40 C41 
> C42 C43 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C39 C40 C41 C42 10 9 8 7 1 
> 0.0 5.9 3 0.0 5.9 3 ; dih C38 C39 C40 C41 11 10 9 8 1 0.0 5.9 3 0.0 
> 5.9 3 ; dih C37 C38 C39 C40 12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C36 
> C37 C38 C39 13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C35 C36 C37 C38 14 
> 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C34 C35 C36 C37 15 14 13 12 1 0.0 
> 5.9 3 0.0 5.9 3 ; dih C33 C34 C35 C36 16 15 14 13 1 0.0 5.9 3 0.0 5.9 
> 3 ; dih C32 C33 C34 C35 14 15 16 18 1 0.0 0.4 6 0.0 0.4 6 ; dih C34 
> C33 C32 O31 15 16 18 19 1 180.0 16.7 2 180.0 16.7 2 ; dih C33 C32 O31 
> C13 32 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih C14 C13 O31 C32 18 19 20 
> 21 1 0.0 5.9 3 0.0 5.9 3 ; dih O31 C13 C12 O11 33 32 19 18 1 0.0 5.9 3 
> 0.0 5.9 3 ; dih O15 C14 C13 O31 22 21 20 19 1 0.0 3.8 3 0.0 3.8 3 ; 
> dih P8 O11 C12 C13 20 21 22 25 1 0.0 1.0 3 0.0 1.0 3 ; dih C12 O11 P8 
> O4 20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih C12 O11 P8 O4 26 25 22 21 1 
> 0.0 1.0 3 0.0 1.0 3 ; dih C3 O4 P8 O11 26 25 22 21 1 0.0 3.1 2 0.0 3.1 
> 2 ; dih C3 O4 P8 O11 22 25 26 27 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O4 C3 
> C2 28 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih N1 C2 C3 O4 26 27 28 31 1 
> 0.0 3.8 3 0.0 3.8 3 ; dih C3 C2 N1 C7 19 32 33 34 1 0.0 3.8 3 0.0 3.8 
> 3 ; dih C13 C14 O15 C16 32 33 34 36 1 180.0 16.7 2 180.0 16.7 2 ; dih 
> C14 O15 C16 C17 37 36 34 33 1 0.0 0.4 6 0.0 0.4 6 ; dih C18 C17 C16 
> O15 38 37 36 34 1 0.0 5.9 3 0.0 5.9 3 ; dih C19 C18 C17 C16 39 38 37 
> 36 1 0.0 5.9 3 0.0 5.9 3 ; dih C20 C19 C18 C17 40 39 38 37 1 0.0 5.9 3 
> 0.0 5.9 3 ; dih C21 C20 C19 C18 41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; 
> dih C22 C21 C20 C19 42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih C23 C22 
> C21 C20 43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih C24 C23 C22 C21 44 43 
> 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih C25 C24 C23 C22 45 44 43 42 1 0.0 
> 5.9 3 0.0 5.9 3 ; dih C26 C25 C24 C23 46 45 44 43 1 0.0 5.9 3 0.0 5.9 
> 3 ; dih C27 C26 C25 C24 47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih C28 
> C27 C26 C25 48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih C29 C28 C27 C26 49 
> 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C29 C28 C27 50 49 48 47 1 0.0 
> 5.9 3 0.0 5.9 3 ; dih C10 C9 C29 C28 MDP FILE: title = vals cpp = 
> /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep 
> dt = 0.002 ; ps ! nsteps = 500 nstlists = 10 ns_type = grid rlist = 
> 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 
> fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 
> pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy 
> minimizing stuff ; emtol = 100.0 emsteps = 0.01
>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================