Hi
Thank you for your reply. After carefully observing the prmtop files I feel
that water residues which I have intentionally kept in protein complex are
creating the problem. Actually I wanted to see whether if any change occurs
in energy values if I retain crystal waters but it is creating problem in
extracting the energies. So is it possible to remove the water residues from
the complex prmtop file and rerun the calculation? or should I do the MMPBSA
from begining again, this time stripping off all the crystal waters. I am
pasting part of the complex prmtop file below, Please suggest if I can do
any changes or rerun the simulation.
%VERSION VERSION_STAMP = V0001.000 DATE = 04/16/10
08:49:32
%FLAG
TITLE
%FORMAT(20a4)
%FLAG
POINTERS
%FORMAT(10I8)
5155 18 2602 2617 5832 3557 11011 8905
0 0
28420 334 2617 3557 8905 60 117 49
43 1
0 0 0 0 0 0 0 0
37 0
0
%FLAG
ATOM_NAME
%FORMAT(20a4)
N H1 H2 H3 CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O
N
H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 OG HG C
O
N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1
HH11HH12NH2
HH21HH22C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22
HD23C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22HD23
C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22HD23C
O N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA
CB
HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA2 HA3 C O N H CA
HA
CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3
CE
HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 SD
CE
HE1 HE2 HE3 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O
N
H CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N
H
CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H
CA
HA2 HA3 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22
HD23C O N H CA HA2 HA3 C O N H CA HA CB HB CG2
HG21HG22HG23
OG1 HG1 C O N H CA HA CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2
CH2
HH2 CZ3 HZ3 CE3 HE3 CD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD
HD2
HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 OG HG
C
O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N CD HD2 HD3
CG
HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA2 HA3 C O N H CA
HA
CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB
CG1
HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB CG2
HG21HG22HG23OG1
HG1 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N
H
CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB CG1 HG11HG12HG13CG2
HG21
HG22HG23C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2
HE3
NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB CG1 HG11HG12HG13CG2
HG21HG22HG23
C O N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB CG2
HG21
HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2 HB3 CG
OD1
OD2 C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O
N
H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ
OH
HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2
HD3
NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB2 HB3 CG
ND1
CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB CG2 HG21HG22HG23CG1
HG12
HG13CD1 HD11HD12HD13C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O
N
H CA HA CB HB2 HB3 SG HG C O N H CA HA CB HB1 HB2 HB3 C
O
N H CA HA CB HB2 HB3 CG ND1 CE1 HE1 NE2 HE2 CD2 HD2 C O N H
CA
HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB2
HB3
CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 HB3 CG
OD1
ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C
O
N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB CG1
HG11HG12HG13CG2
HG21HG22HG23C O N H CA HA2 HA3 C O N H CA HA CB HB CG1
HG11
HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB1 HB2 HB3 C O N
H
CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H
CA
HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG2 HG3
CD
HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 CG
HG
CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG2
HG3
CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG2 HG3
CD
OE1 NE2 HE21HE22C O N H CA HA CB HB CG1 HG11HG12HG13CG2
HG21HG22HG23
C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N
H
CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C
O
N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1
HH11HH12NH2
HH21HH22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O
N
H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB
HB2
HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2
HB3
CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB HB
CG2
HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB CG1
HG11
HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 OG HG C O
N
H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3
C
O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C
O
N H CA HA CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3
CE3
HE3 CD2 C O N H CA HA CB HB2 HB3 SG HG C O N H CA HA
CB
HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB HB2 HB3 CG CD1 HD1
CE1
HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG ND1
CE1
HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1
OE2
C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ
HZ1
HZ2 HZ3 C O N H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG
HG
CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG1
HG11HG12HG13
CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3
CE
HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA2 HA3 C O N H CA HA
CB
HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 SG HG C O N H CA
HA
CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2
HB3
CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA
CB
HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB HB2 HB3 CG HG CD1
HD11
HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG C O
N
H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG
HG
CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG2
HG3
CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3
CG
HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG
OD1
OD2 C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2
HE2
CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22
HD23C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA
CB
HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB
HB2
HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA
CB
HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB
HB
CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2
HB3
CG ND1 CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG CD1
HD1
NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C O N CD HD2 HD3 CG
HG2
HG3 CB HB2 HB3 CA HA C O N H CA HA CB HB CG2 HG21HG22HG23OG1
HG1
C O N H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG CD1 HD1
CE1
HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3
CD
HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N CD HD2 HD3 CG HG2 HG3 CB
HB2
HB3 CA HA C O N H CA HA2 HA3 C O N H CA HA CB HB2 HB3
CG
HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG CD1 HD1
CE1
HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG CD1 HD1
CE1
HE1 CZ HZ CE2 HE2 CD2 HD2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3
CA
HA C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22HD23
C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 OG HG C
O
N H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG OD1 ND2
HD21HD22C
O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H
CA
HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N CD HD2 HD3 CG HG2
HG3
CB HB2 HB3 CA HA C O N H CA HA CB HB2 HB3 OG HG C O N
H
CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB CG2
HG21HG22HG23
OG1 HG1 C O N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N
H
CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H
CA
HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA
HA
CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB CG2 HG21HG22HG23OG1
HG1
C O N H CA HA CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2
CZ3
HZ3 CE3 HE3 CD2 C O N H CA HA CB HB1 HB2 HB3 C O N H CA
HA
CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1
HE2
HE3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N
H
CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2
HB3
CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG1
HG11
HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 CG OD1 OD2 C
O
N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA2
HA3
C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22HD23C
O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H
CA
HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O
N
H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB CG2
HG21HG22HG23CG1
HG12HG13CD1 HD11HD12HD13C O N H CA HA2 HA3 C O N H CA HA
CB
HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB
HB2
HB3 OG HG C O N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O
N
H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O
N
H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA CB HB2
HB3
CG ND1 CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG
CD1
HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG2 HG3
CD
OE1 NE2 HE21HE22C O N H CA HA CB HB CG1 HG11HG12HG13CG2
HG21HG22HG23
C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H
CA
HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB
HB
CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2
HB3
CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3
CG
OD1 ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3
CE
HE2 HE3 NZ HZ1 HZ2 HZ3 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA
HA
C O N H CA HA2 HA3 C O N H CA HA CB HB2 HB3 CG HG CD1
HD11
HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD
HD2
HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 CG CD1
HD1
CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG
HG2
HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N CD HD2 HD3 CG HG2
HG3
CB HB2 HB3 CA HA C O N H CA HA CB HB1 HB2 HB3 C O N H
CA
HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB2
HB3
CG OD1 ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1
NE2
HE21HE22C O N H CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1
HD11HD12
HD13C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N
H
CA HA CB HB2 HB3 SG HG C O N H CA HA CB HB2 HB3 CG ND1 CE1
HE1
NE2 HE2 CD2 HD2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C
O
N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2
C
O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C
O
N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 HB3 CG
HG2
HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3
CE
HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 CG HG CD1
HD11HD12
HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG2 HG21HG22HG23CG1
HG12HG13
CD1 HD11HD12HD13C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2
HE21
HE22C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH CE2
HE2
CD2 HD2 C O N H CA HA CB HB2 HB3 SG HG C O N H CA HA
CB
HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O N H CA HA CB HB2 HB3
OG
HG C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3
NZ
HZ1 HZ2 HZ3 C O N H CA HA2 HA3 C O N H CA HA CB HB CG2
HG21
HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB CG1
HG11HG12
HG13CG2 HG21HG22HG23C O N H CA HA CB HB CG1 HG11HG12HG13CG2
HG21HG22
HG23C O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H
CA
HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1
CZ
OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 OG HG C O
N
CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB HB2
HB3
CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA2 HA3 C O
N
H CA HA CB HB2 HB3 OG HG C O N CD HD2 HD3 CG HG2 HG3 CB HB2
HB3
CA HA C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA
HA
CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C
O
N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB
HB2
HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C O N
H
CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD
HD2
HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N CD HD2 HD3 CG HG2 HG3 CB HB2
HB3
CA HA C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O
N
H CA HA CB HB2 HB3 CG OD1 OD2 C O N CD HD2 HD3 CG HG2 HG3 CB
HB2
HB3 CA HA C O N H CA HA CB HB2 HB3 OG HG C O N H CA
HA
CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA
CB
HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB
HB2
HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG OD1 OD2
C
O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA
CB
HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O
N
H CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N
H
CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C
O
N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB CG2
HG21HG22HG23
CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB1 HB2 HB3 C O
N
H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG2 HG3
CD
HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 CG
ND1
CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG OD1 ND2
HD21HD22
C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ
HZ1
HZ2 HZ3 C O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N
H
CA HA CB HB CG2 HG21HG22HG23OG1 HG1 C O N H CA HA CB HB1 HB2
HB3
C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21HE22C O
N
H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA
CB
HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB
HB
CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N H CA HA CB HB2
HB3
CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H
CA
HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O N CD
HD2
HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O N H CA HA CB HB2 HB3 CG
HG2
HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD
OE1
NE2 HE21HE22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE
HE
CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB2 HB3 CG OD1 ND2
HD21
HD22C O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2
HD21HD22HD23
C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N
H
CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB
HB
CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C O N CD HD2 HD3 CG HG2
HG3
CB HB2 HB3 CA HA C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2
HD3
CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 OG HG C
O
N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA
HA
CB HB CG2 HG21HG22HG23OG1 HG1 C O N CD HD2 HD3 CG HG2 HG3 CB HB2
HB3
CA HA C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O
N
H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2
HH21
HH22C O N H CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1
HD11HD12HD13
C O N H CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3
CG
HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG OD1 ND2
HD21HD22C
O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2
C
O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1
HZ2
HZ3 C O N H CA HA CB HB CG1 HG11HG12HG13CG2 HG21HG22HG23C O
N
H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O
N
H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG
CD1
HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG
HG2
HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG HG CD1
HD11HD12HD13CD2
HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG C O N H CA
HA
CB HB2 HB3 OG HG C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1
NE2
HE21HE22C O N H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA
HA
CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N H CA HA CB HB
CG2
HG21HG22HG23OG1 HG1 C O N H CA HA CB HB CG2 HG21HG22HG23OG1 HG1
C
O N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C
O
N H CA HA CB HB2 HB3 CG HG CD1 HD11HD12HD13CD2 HD21HD22HD23C O
N
H CA HA CB HB2 HB3 OG HG C O N H CA HA CB HB2 HB3 CG CD1
HD1
CE1 HE1 CZ OH HH CE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG
OD1
ND2 HD21HD22C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE
HE
CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB2 HB3 CG OD1 ND2
HD21
HD22C O N H CA HA CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2
HH2
CZ3 HZ3 CE3 HE3 CD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD HD2
HD3
NE HE CZ NH1 HH11HH12NH2 HH21HH22C O N H CA HA CB HB CG1
HG11HG12
HG13CG2 HG21HG22HG23C O N H CA HA CB HB2 HB3 SG HG C O N
H
CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB2 HB3 CG HG CD1
HD11HD12
HD13CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 CG HG CD1
HD11HD12HD13
CD2 HD21HD22HD23C O N H CA HA CB HB2 HB3 OG HG C O N H
CA
HA CB HB2 HB3 SG HG C O N H CA HA CB HB CG2 HG21HG22HG23OG1
HG1
C O N H CA HA CB HB2 HB3 OG HG C O N H CA HA CB HB2
HB3
CG ND1 CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA HA CB HB2 HB3 CG HG2
HG3
CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3
CG
OD1 OD2 C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ OH HH
CE2
HE2 CD2 HD2 C O N CD HD2 HD3 CG HG2 HG3 CB HB2 HB3 CA HA C O
N
H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ HZ CE2 HE2 CD2 HD2 C O
N
H CA HA CB HB2 HB3 CG ND1 CE1 HE1 NE2 HE2 CD2 HD2 C O N H CA
HA
CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG
HG2
HG3 CD OE1 OE2 C O N H CA HA CB HB2 HB3 CG CD1 HD1 CE1 HE1 CZ
HZ
CE2 HE2 CD2 HD2 C O OXT O33 C32 O34 C20 H201H202O15 C4 C2 H2 C5 F9
C6
H6 C3 H3 C7 C11 O16 N36 HN3 C18 H181H182C13 S22 N21 C26 C24 C27 F14 C28
H28
C25 F8 C29 F23 O H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2
O
H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1
H2
O H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2
On Tue, Apr 20, 2010 at 9:11 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Tue, Apr 20, 2010 at 11:08 AM, Hyma vathi <hymavathi.niper.gmail.com
> >wrote:
>
> > Thank you for the reply. But I am unable to find where the error is. The
> > solvated prmtop is consistent with the trajectory i have given in -y
> flag.
> > But for the mdcrds the MMPBSA.py created the structures were distorted.
> The
> > masks are matching in the namelist. Please let me know how can I spot the
> > error I tried to attach the prmtop files but failed.
> >
>
> You should not have to specify the masks anymore. As long as the ligand
> residues appear as a continuous sequence in the complex topology file,
> MMPBSA.py will correctly guess the appropriate masks for the ligand and
> receptor. It will also print out the guessed mask in the final output file
> so you can check it. Note that this is a good error check. If MMPBSA.py
> fails to correctly guess the mask, it is likely that your topology files
> are
> inconsistent.
>
> Note, too, that it's not just important for the solvated_prmtop to be
> consistent with the mdcrd passed to MMPBSA.py. It is also important that
> the complex_prmtop, receptor_prmtop, and ligand_prmtop be consistent with
> _MMPBSA_complex.mdcrd, _MMPBSA_receptor.mdcrd, and _MMPBSA_ligand.mdcrd,
> respectively. If these structures look warped and/or distorted, then your
> prmtops are inconsistent. Here are a couple things to look out for:
>
> Any waters and/or ions present in your solvated_prmtop are stripped, and so
> should not be present in any other topology file (complex, receptor, or
> ligand). The number of atoms in the complex prmtop must equal the sum of
> the number of atoms in the receptor_prmtop plus the number of atoms in the
> ligand_prmtop. (This will be checked for automatically in a future release
> of MMPBSA.py).
>
> Good luck!
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Hymavathi,
MS(Pharm),
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education and Research(NIPER),
Mohali,
INDIA.
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Received on Wed Apr 21 2010 - 09:00:02 PDT
