Hi! I have two phosphorylated serines which form part of peptide that I want to perform simulated annealing. But the catch is the SEP group is read as a Non-Protein and so it is present in two T-coupling groups, the Non-Potein and the protein group I want to heat. I need to remove this group (SEP-phosphorylated serine) from the Non-Protein group. The Non-Protein group contains about 20,000 atoms (water, counterions and also the SEP group). So how can I remove this group from the Non-Protein group? Welcoming your suggestions Jayant James
On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jayant james wrote: > >> 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? >> > > You will need to make special index groups, i.e.: > > r 1-x (for the appended segment) > r x-y (the rest of the protein) > > These groups can be used as your tc-grps. > > -Justin > > 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 < >> http://www.chick.com/reading/tracts/0096/0096_01.asp>) >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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://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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp)
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