[gmx-users] parameter on Energy Minimization

[Justin A. Lemkul]

Quoting Liu Shiyong <liushiyong at gmail.com>:

> Hi,
>
> I used a script given below for energy minimization of  a native
> protein-protein complex 1akj.
>
> I removed HETATMs and water molecules from the structure, and the minimized
> structure  (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.
> Then I used rasmol to check the result.  The ligand is ran away from
> receptor.
>  rasmol 1akj_oplsaa.minim_traj.pdb

I think you might be seeing a visualization artifact from PBC.  How large is the
box you are using?  Typically, when I do an in vacuo minimization, I place my
solute in a large box (using editconf) to prevent interactions with periodic
images; often times the box dimensions automatically given to your protein fit
quite tightly to the size of the system.

-Justin

>
>
> Then I tried the larger epsilon_r           =  800000.0, and got very
> similar result. I mean that for two substantially different values of the
> epsilon_r minimization gives absolutely the same final positions of the
> ligand.
>
> I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,
> G45a3, G53a5, G53a6,  gmx, oplsaa.
> I also got similar result.
>
>
> script:
>
> pdb2gmx   -ff oplsaa -f 1akj_oplsaa.pdb -p 1akj_oplsaa.top -o
> 1akj_oplsaa.gro -i 1akj_oplsaa.itp > 1akj_oplsaa.
> output.pdb2gmx 2>&1 &
>
> grompp -f em.mdp -c 1akj_oplsaa.gro -p 1akj_oplsaa.top -o
> 1akj_oplsaa.input.tpr > 1akj_oplsaa.output.grompp
> 2>&1 &
>
> mdrun -nice 0 -v -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.trr -c
> 1akj_oplsaa.minimized.gro -e
> 1akj_oplsaa.
>
> minim_ener.edr > 1akj_oplsaa.output.mdrun 2>&1 &
>
>  trjconv  -f 1akj_oplsaa.minim_traj.trr -s 1akj_oplsaa.input.tpr -o
> 1akj_oplsaa.minim_traj.pdb << HHH
> 2
> 2
> HHH
>
>
> em.mdp is :
>
> title               =  1akj_oplsaa
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  cut-off
> epsilon_r           =  80.0
> rcoulomb            =  1.8
> vdwtype             =  cut-off
> rvdw                =  1.8
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  10.0
> emstep              =  0.01
>
>
>
>
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>



========================================

Justin A. Lemkul
Graduate Research Assistant
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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