Hi ! I am attempting to do a simulated annealing and running into problem. Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. So I ligated the NMR structure to the crystal structure and in an attempt to find the correct orientation of the NMR segment in the crystal structure I planned to do a simulated annealing run specifically to this ligated NMR segment. Having ligated this NMR segment to the crystal structure I gave the pdb2gmx command, then created a box, filled it with water and performed a distance restrained energy minimization (wherein I input some FRET distances as distance restraints). Its all fine till this step. Now I create an index group that has the NMR group as the third group in the temperature coupling, the other two are Protein and Non-Protein. when I run the grompp to start a simulated annealing run I get a message stating that the NMR group's atoms are also found in the Protein group. Gromacs is right in detecting this problem. As I cannot have the same amino acids in 2 different groups which are coupled to two different temperatures. So how am I to attempt this simulated annealing because the program does not want to have the NMR group present in the Protein group? So say I delete the NMR segment that was appended to the crystal structure how and which stage do I integrate the NMR group that I wanted to perform the simulated annealing on, into the system? Thanks Jayant
*The pr.mdp file is as below* ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein NMR-group tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein Non-Protein NMR-group ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; ; ; ;simulated annealing ;Type of annealing form each temperature group (no/single/periodic) annealing = no no single ; ;Number of annealing points to use for specifying annealing in each group annealing_npoints 0 0 9 ; ; List of times at the annealing points for each group annealing_time = 0 25 50 75 100 125 150 175 200 ; Temp.at each annealing point, for each group. annealing_temp = 300 350 400 450 500 450 400 350 300 *The error messge is given below* creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_D 1 Excluding 2 bonded neighbours for SOL 72948 Excluding 1 bonded neighbours for NA+ 214 Excluding 1 bonded neighbours for CL- 207 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 4588 # G96ANGLES: 6638 # PDIHS: 2521 # IDIHS: 2044 # LJ14: 7634 # DISRES: 22 # SETTLE: 72948 initialising group options... processing index file... WARNING 1 [file "new.top", line 28039]: T-Coupling group Protein has fewer than 10% of the atoms (4550 out of 223817) Maybe you want to try Protein and Non-Protein instead? WARNING 2 [file "new.top", line 28039]: T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of 223817) Maybe you want to try Protein and Non-Protein instead? ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: readir.c, line: 843 Fatal error: Atom 2589 in multiple T-Coupling groups (1 and 3) ------------------------------------------------------- ** ** *The commands that I use are given below* ** #pdb2gmx -f start.pdb -p new -o new -ignh -merge #creating a box and addition of water molecules #editconf -f new.gro -o out -c -princ -d 2.2 #genbox -cp out -cs -o check #editconf -f check -o check.pdb #rasmol check.pdb #Energy minimization and addition of ions to neutralise the system #grompp -f em.mdp -c check -p new.top -o em.tpr #genion -s em.tpr -o next -p new -random -g -neutral -conc 0.15 #pname -Na -np 13 #editconf -f next.gro -o next.pdb #rasmol next.pdb #option 13 for SOL #Running the EM. Here change the Na to NA+ in topology file and I/P *.gro file. #grompp -f em.mdp -c next.gro -p new.top -o em.tpr #mdrun -v -s em -x em -o em -c em.gro & #editconf -f em.gro -o em.pdb #rasmol em.pdb *This is where the problem begins* #Running MD. grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index #mdrun -s pr -e pr -g md -o traj.trr -c pr.gro & #extending #tpbconv -s ../pr.tpr -f 300.xtc -e ../ener.edr -o 1ns.tpr -until 1000 #mdrun -s 1ns.tpr -o 1ns.trr & -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp)
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