[gmx-users] how to get a minimized structure pdb

[Mark Abraham]

On 03/04/12, balaji nagarajan <balaji_sethu at hotmail.com> wrote:

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> Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
> ------------ 
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> --------------------
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL     0 
> 
> MODEL     1
> 
> MODEL      2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --------------------------------------
> define               = -DFLEXIBLE
> constraints          = none
> integrator           = cg
> dt                   = 0.001     ; ps !
> nsteps               = 1000
> nstlist              = 10
> ns_type              = grid
> rlist                = 1.0
> coulombtype          = PME
> rcoulomb             = 1.0
> vdwtype              = cut-off
> rvdw                 = 1.0
> optimize_fft         = yes
> ;
> ;        Energy minimizing stuff
> ;
> emtol                = 10.0
> emstep               = 0.01
> 
> energygrps = protein SOL
> ----------------------------------------
> 
> thanks in advance Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
> ------------ 
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> --------------------
> 
> 

 
That will convert the contents of the trajectory file into a pseudo-trajectory in .pdb format. Hence you see multiple models. So you can simply look only at the last model, or direct trjconv to only convert the last trajectory frame, or perhaps use the file written by mdrun -c. You could have pre-solved the problem by writing the -c file in .pdb format by choosing mdrun -s yourem.tpr -c yourfinalstructure.pdb. 
 
Mark 
 

> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
> ------------ 
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> --------------------
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL     0 
> 
> MODEL     1
> 
> MODEL      2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --------------------------------------
> define               = -DFLEXIBLE
> constraints          = none
> integrator           = cg
> dt                   = 0.001     ; ps !
> nsteps               = 1000
> nstlist              = 10
> ns_type              = grid
> rlist                = 1.0
> coulombtype          = PME
> rcoulomb             = 1.0
> vdwtype              = cut-off
> rvdw                 = 1.0
> optimize_fft         = yes
> ;
> ;        Energy minimizing stuff
> ;
> emtol                = 10.0
> emstep               = 0.01
> 
> energygrps = protein SOL
> ----------------------------------------
> 
> thanks in advance Dear Users ! 
> 
> I have done a minimization for a tetrapeptide in a water box
> 
> with conjugate gradient minimization of 1000 steps
> 
> when I convert it to pdb as below 
> ------------ 
> 
> trjconv -f em.trr -o min.pdb -s em.tpr << EOF
> 0
> EOF
> --------------------
> 
> the out put pdb has many structures 
> as follows 
> 
> MODEL     0 
> 
> MODEL     1
> 
> MODEL      2  
> 
> but the minimized pdb is single structre , 
> 
> what does these structures mean. 
> 
> how to obtain a single structre. 
> 
> my mimization input file is as follows
> --------------------------------------
> define               = -DFLEXIBLE
> constraints          = none
> integrator           = cg
> dt                   = 0.001     ; ps !
> nsteps               = 1000
> nstlist              = 10
> ns_type              = grid
> rlist                = 1.0
> coulombtype          = PME
> rcoulomb             = 1.0
> vdwtype              = cut-off
> rvdw                 = 1.0
> optimize_fft         = yes
> ;
> ;        Energy minimizing stuff
> ;
> emtol                = 10.0
> emstep               = 0.01
> 
> energygrps = protein SOL
> ----------------------------------------
> 
> thanks in advance 
> 
> 
> 
> 

 
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