sorry, but i forgot to say that the distance between this tyrosine and the P of the DNA was from a previously calculated MD simulation. when i tried to add the following line into the (see below) mdp file: table-extension = 2 the warning messages becomes
Warning: 1-4 interaction between 8159 and 8184 at distance 2.017 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, these atoms correspond to the interesting P of my DNA and C4' of the previous nucleotide in the DNA any suggestions ? thanks very lot joern ---------- Forwarded Message ---------- Subject: Warning: 1-4 interaction Date: Thursday 12 April 2007 16:35 From: Joern Lenz <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] dear gromacs guys, i have the following problem: i linked the phosphate atom of a DNA to the phenolic-hydroxyl group of a proteins tyrosine by defining a line in the specbond.dat file. the distance before linking these atoms was about 4.2 angstroms. my intention now was first to minimize the linked complex using the following mdp file: integrator = steep dt = 0.002 nsteps = 400 nstenergy = 5 nstxtcout = 5 nstlist = 5 ns_type = simple rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes constraints = none emtol = 1.0 emstep = 0.0005 starting the minimzation the following warning occurs - and i know that this problem was discussed often before : Warning: 1-4 interaction between 1435 and 8183 at distance 1.862 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 i know what this error message means. Their 1-4 distance is too long. the mentioned atoms are of the DNA and the tyrosine respectively. my question now is: how can i fix this warning ? since i run minimzation and this warning occurs i do not know exactly how to go on becuase i run minimization in order to shrink the bond-length between protein and dna. how else can i shrink it to avoid the warning ? does anyone has an idea that would help me to gon on with my work ? thanks a lot in advance and have a nice spring-day evening greetings joern ------------------------------------------------------- _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
