Dear Case
Since two strands of dna had separated, com.xtc trajectory file was obtained
from -pbc nojump and -pbc mol in gromacs.
1) at first, I open a com.pdb file (containing protein, dna, water and
Na+)and a trajectory file of gromacs (com.xtc)by VMD.
then I saved trajectory as com.mdcrd file by vmd.
I made some changes in com.pdb file: 1) I changed SOL to WAT. 2) I changed
OW, HW1, HW2 to O, H1, H2
and I named that com_modify.pdb
2) in amber I used following
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
com = loadpdb "com_modify.pdb"
saveamberparm com com.prmtop com.inpcrd
3)I opened created com.prmtop file and converted com.mdcrd trajectiry file
by vmd.
my simulation box in gromacs is cubic with 6 nm dimension.
I used image and center before in amber as follows (1-86 are residues
relating to protein and dna):
trajin full.mdcrd
trajout full_ic.mdcrd
center :1-86
image center
but problem was not solved.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Mon Dec 27 2010 - 07:00:04 PST
