[gmx-users] problem_with_rewritting_pdb

[Justin A. Lemkul]

balaji nagarajan wrote:
> Dear Users !
> 
> I have minimized the attached file using the gromacs43a1 and oplsaa 
> force field using spc water molecules
> 
> I have used the following script for generating topology .
> i minimized for 2000 steps , my doubt is when i rewrite the minimized 
> pdb , in case of oplsaa
> i was able to get all atoms , but in the case of the gromacs43a1 i am 
> not getting the hydrogen atoms of the protein ,
> 
> how to solve this
> 

http://www.gromacs.org/Documentation/Terminology/Force_Fields/United_Atom_Force_Field

-Justin

> here is the steps which i have used
> 
> -------------------------------
> pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water spc
> editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
> genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
> grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
> mdrun -v -deffnm em
> trjconv -f em.trr -o min.pdb -s em.tpr ( in this i gave the option 0 for 
> the total system)
> ------------------------------------------------------------------
> the minim.mdp
> 
> 
> define               = -DFLEXIBLE
> constraints          = none
> integrator           = steep
> dt                   = 0.002     ; ps !
> nsteps               = 2000
> 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
> -----------------------------------------------
> 
> 
> thanks in advance
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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