[gmx-users] problem_with_rewritting_pdb

balaji nagarajan balaji_sethu at hotmail.com
Mon Oct 10 21:06:03 CEST 2011

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 

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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