Dear amber
users
merry
christmas
I did simulation in gromacs. I converted gromacs trajrctory file (xtc) to
amber trajectory file (mdcrd) by VMD
to do some analysis. I want to obtain .prmtop file. I have a pdb file
containing protein and water (TIP3P model).
in pdb file water molecules are as
follows:
ATOM 24068 O WAT 7487 57.300 0.280 45.070 1.00
0.00
ATOM 24069 H1 WAT 7487 56.970 0.430 44.190 1.00
0.00
ATOM 24070 H2 WAT 7487 58.180 0.660 45.060 1.00
0.00
ATOM 24071 O WAT 7488 54.080 7.820 1.430 1.00
0.00
ATOM 24072 H1 WAT 7488 53.930 6.900 1.180 1.00
0.00
ATOM 24073 H2 WAT 7488 54.840 8.080 0.910 1.00
0.00
ATOM 24074 O WAT 7489 50.570 51.250 54.030 1.00
0.00
ATOM 24075 H1 WAT 7489 50.380 51.730 53.230 1.00
0.00
ATOM 24076 H2 WAT 7489 51.410 50.820 53.870 1.00
0.00
when I
use
com = loadpdb
"com.pdb"
saveamberparm com com.prmtop
com.inpcrd
-- ignoring the
warnings.
Building
topology.
Building atom
parameters.
Building bond
parameters.
Building angle
parameters.
Building proper torsion
parameters.
Building improper torsion
parameters.
total 359 improper torsions
applied
Building H-Bond
parameters.
Not Marking per-residue atom chain
types.
Marking per-residue atom chain
types.
(Residues lacking connect0/connect1
-
*these don't have chain types marked*:
res total
affected
CGLY
1
NGLY
1
WAT
7406
)
(no
restraints)
when I load created .prmtop and converted .mdcrd files by VMD, there is
problem only in water molecules.
1) the length of O-H bonds are longer than those of normal waters. 2) there
are new bonds between H atoms
of each water
molecule.
is this state normal? is it a visual program? Do trajectory file
conversion
done correctly? how to fix it?
I need .prmtop file for some anlysis in
ptraj.
is there problem in .prmtop file? (meybe, it doesn't match with trajectory
about waters)
any help will highly apprecited.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Sun Dec 26 2010 - 03:30:03 PST
