[gmx-users] Simulated annealing

jayant james jayant.james at gmail.com
Mon Mar 23 20:34:35 CET 2009


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 <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>)
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> 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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-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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