[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules

From: leila karami <karami.leila1.gmail.com>
Date: Mon, 27 Dec 2010 18:10:14 +0330

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
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