<div>Hi!</div>
<div>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? </div>
<div>Welcoming your suggestions</div>
<div>Jayant James</div>
<div><br><br> </div>
<div class="gmail_quote">On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="im"><br><br>jayant james wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi !<br>I am attempting to do a simulated annealing and running into problem.<br>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.<br>
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?<br>
</blockquote><br></div>You will need to make special index groups, i.e.:<br><br>r 1-x (for the appended segment)<br>r x-y (the rest of the protein)<br><br>These groups can be used as your tc-grps.<br><br>-Justin<br><br>
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<div class="h5">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?<br> Thanks<br>
Jayant<br> *The pr.mdp file is as below*<br> <br>; Berendsen temperature coupling is on in two groups<br><br>Tcoupl = Berendsen<br><br>tc-grps = Protein Non-Protein NMR-group <br>tau_t = 0.1 0.1 0.1<br>
<br>ref_t = 300 300 300<br><br>; Energy monitoring<br><br>energygrps = Protein Non-Protein NMR-group<br>; Pressure coupling is not on<br><br>Pcoupl = parrinello-rahman<br>
<br>tau_p = 0.5<br><br>compressibility = 4.5e-5<br><br>ref_p = 1.0<br><br>; Generate velocites is on at 300 K.<br><br>gen_vel = yes<br><br>gen_temp = 300.0<br><br>
gen_seed = 173529<br><br>;<br><br>;<br><br>;<br><br>;simulated annealing<br><br>;Type of annealing form each temperature group (no/single/periodic)<br><br>annealing = no no single<br><br>;<br><br>;Number of annealing points to use for specifying annealing in each group<br>
<br>annealing_npoints 0 0 9<br><br>;<br><br>; List of times at the annealing points for each group<br><br>annealing_time = 0 25 50 75 100 125 150 175 200<br><br>; Temp.at each annealing point, for each group.<br>
<br>annealing_temp = 300 350 400 450 500 450 400 350 300<br> *The error messge is given below*<br> <br> <br>creating statusfile for 1 node...<br><br> <br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#<br><br>
checking input for internal consistency...<br><br>calling /usr/bin/cpp...<br><br>processing topology...<br><br>Generated 279 of the 1225 non-bonded parameter combinations<br><br>Excluding 3 bonded neighbours for Protein_D 1<br>
<br>Excluding 2 bonded neighbours for SOL 72948<br><br>Excluding 1 bonded neighbours for NA+ 214<br><br>Excluding 1 bonded neighbours for CL- 207<br><br>processing coordinates...<br><br>double-checking input for internal consistency...<br>
<br>Velocities were taken from a Maxwell distribution at 300 K<br><br>renumbering atomtypes...<br><br>converting bonded parameters...<br><br># G96BONDS: 4588<br><br># G96ANGLES: 6638<br><br># PDIHS: 2521<br>
<br># IDIHS: 2044<br><br># LJ14: 7634<br><br># DISRES: 22<br><br># SETTLE: 72948<br><br>initialising group options...<br><br>processing index file...<br><br>WARNING 1 [file "new.top", line 28039]:<br>
<br> T-Coupling group Protein has fewer than 10% of the atoms (4550 out of<br><br> 223817)<br><br> Maybe you want to try Protein and Non-Protein instead?<br><br>WARNING 2 [file "new.top", line 28039]:<br><br> T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of<br>
<br> 223817)<br><br> Maybe you want to try Protein and Non-Protein instead?<br><br> <br>-------------------------------------------------------<br><br>Program grompp, VERSION 3.3.3<br><br>Source code file: readir.c, line: 843<br>
<br> <br>Fatal error:<br><br>Atom 2589 in multiple T-Coupling groups (1 and 3)<br><br>-------------------------------------------------------<br><br>** ** *The commands that I use are given below*<br>** #pdb2gmx -f start.pdb -p new -o new -ignh -merge<br>
<br> <br> <br>#creating a box and addition of water molecules<br><br> <br>#editconf -f new.gro -o out -c -princ -d 2.2<br><br>#genbox -cp out -cs -o check<br><br>#editconf -f check -o check.pdb<br><br>#rasmol check.pdb<br>
<br> <br> <br>#Energy minimization and addition of ions to neutralise the system<br><br> <br>#grompp -f em.mdp -c check -p new.top -o em.tpr<br><br>#genion -s em.tpr -o next -p new -random -g -neutral -conc 0.15 #pname -Na -np 13<br>
<br>#editconf -f next.gro -o next.pdb<br><br>#rasmol next.pdb<br><br> <br>#option 13 for SOL<br><br> <br>#Running the EM. Here change the Na to NA+ in topology file and I/P *.gro file.<br><br> <br>#grompp -f em.mdp -c next.gro -p new.top -o em.tpr<br>
<br>#mdrun -v -s em -x em -o em -c em.gro &<br><br>#editconf -f em.gro -o em.pdb<br><br>#rasmol em.pdb<br><br> <br>*This is where the problem begins*<br><br>#Running MD.<br><br>grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index<br>
<br>#mdrun -s pr -e pr -g md -o traj.trr -c pr.gro &<br><br> <br>#extending<br><br>#tpbconv -s ../pr.tpr -f 300.xtc -e ../ener.edr -o 1ns.tpr -until 1000<br><br>#mdrun -s 1ns.tpr -o 1ns.trr &<br><br><br><br>-- <br>
Jayasundar Jayant James<br><br></div></div><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">www.chick.com/reading/tracts/0096/0096_01.asp</a> <<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">http://www.chick.com/reading/tracts/0096/0096_01.asp</a>>)<br>
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</blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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