Dear amber users
I did simulation of protein-dna complex by gromacs. I want to do hydrogen
bond analysis by amber, I know for that I need to .prmtop and .mdcrd files.
I converted gromacs trajectory file (.xtc) to .mdcrd file by VMD.
I want to create .prmtop and .inpcrd files for my pdb file (containing
protein + dna + water + Na). I'm using amber03
forcefield. first and last protein residues in my pdb are as follows:
ATOM 1 N GLY 1 26.110 41.200 17.610 1.00 0.00
ATOM 2 CA GLY 1 24.840 40.900 18.290 1.00 0.00
ATOM 3 2HA GLY 1 24.150 41.740 18.280 1.00 0.00
ATOM 4 3HA GLY 1 25.220 40.740 19.300 1.00 0.00
ATOM 5 C GLY 1 24.170 39.640 17.780 1.00 0.00
ATOM 6 O GLY 1 24.490 39.140 16.700 1.00 0.00
.
.
.
ATOM 1035 N GLY 60 35.450 46.770 38.960 1.00 0.00
ATOM 1036 H GLY 60 35.810 46.010 38.390 1.00 0.00
ATOM 1037 CA GLY 60 36.430 47.230 39.920 1.00 0.00
ATOM 1038 2HA GLY 60 35.990 47.260 40.920 1.00 0.00
ATOM 1039 3HA GLY 60 36.850 48.200 39.670 1.00 0.00
ATOM 1040 C GLY 60 37.680 46.390 40.110 1.00 0.00
ATOM 1041 O GLY 60 37.810 45.380 39.370 1.00 0.00
after loadpdb file:
Added missing heavy atom: .R<CGLY 60>.A<OXT 8>
total atoms in file: 24095
Leap added 4 missing atoms according to residue templates:
1 Heavy
3 H / lone pairs
thus, 24099 atoms should be in .prmtop and .inpcrd files. is it true?
and after saveamberparm:
-- 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)
is there problem?
when I visualize my generated .prmtop and .inpcrd files by VMD, it differs
from initial pdb file (there are
undesirable bonds between atoms)
how to fix it?
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Received on Sat Dec 11 2010 - 04:00:02 PST
