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
--
========================================
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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