[gmx-users] Simulated annealing
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 23 21:27:49 CET 2009
jayant james wrote:
> 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?
Add it to aminoacids.dat, and increment the number at the top of the file.
-Justin
> Welcoming your suggestions
> Jayant James
>
>
>
> On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
>
> ------------------------------------------------------------------------
>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
>
> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
--
========================================
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
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