The water residues that you have retained are creating the problems you have
seen. MMPBSA.py automatically strips out all of the water molecules from the
trajectory file, which led to a mismatch between your complex_prmtop and the
complex mdcrd created by MMPBSA.py. If you want to do the calculation with
the water molecules, then you should specify the strip_mask command in the
&general section of the input file to remove only the water molecules that
you do not want to keep. This is a tricky process and needs to be done with
care.
You can certainly remove the water residues from the prmtop using rdparm or
simply create a new complex_prmtop without the water residues present. As
Jason mentioned earlier, if you remove the water molecules, then you should
not have to specify the receptor or ligand masks as MMPBSA.py will be able
to guess those correctly without user input. This should make the
calculation work correctly.
Good luck!
-Bill
On Wed, Apr 21, 2010 at 11:50 AM, Hyma vathi <hymavathi.niper.gmail.com>wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 21 2010 - 09:30:02 PDT
