Hi,
I need to simulate a protein with two manganese ions,I have import the
MN2+ parameters that download from
www.pharmacy.manchester.ac.uk/bryce/amber.Because in my situation the Mn2+
is coordinated both to amino acid both to ligand,so I bond these atoms each
other.
I run desc complex.311.MN/complex.312.MN,the bond looks added now. But
when I runed 'saveamberparm complex ca-pp2a.prmtop ca-pp2a.inpcrd',I got
serveral errors below,I saw Hashem Taha at the maillist that he have got
I1JGM_CD_chg1.prep and 1JGM_CD_sem.frcmod using MCPB,but I have the
questiones: metalParm.xml and metal.xml that in the AMBERHOME/data/metals
could not include the Cd2+ parameters,how do you operate the MCPB to build
the .prep and .frcmod files.I would like your help very much.
> desc complex.311.MN
ATOM
Name: MN
Type: MN
Charge: 2.0000
Polarization: 0.0000
Element: ?
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: -32.867000, -24.239000, 40.178000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<UNK 310>.A<O9 27> by a single bond.
Bonded to .R<ASP 85>.A<OD2 10> by a single bond.
Bonded to .R<HIE 167>.A<NE2 12> by a single bond.
Bonded to .R<HIE 241>.A<ND1 9> by a single bond.
Bonded to .R<ASN 117>.A<OD1 9> by a single bond.
> desc complex.312.MN
ATOM
Name: MN
Type: MN
Charge: 2.0000
Polarization: 0.0000
Element: ?
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: -32.063000, -21.952000, 37.873000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<UNK 310>.A<O15 24> by a single bond.
Bonded to .R<UNK 310>.A<O3 13> by a single bond.
Bonded to .R<UNK 310>.A<O9 27> by a single bond.
Bonded to .R<HIE 59>.A<NE2 12> by a single bond.
Bonded to .R<ASP 85>.A<OD2 10> by a single bond.
Bonded to .R<ASP 57>.A<OD2 10> by a single bond.
> saveamberparm complex ca-pp2a.prmtop ca-pp2a.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -7.999000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: O2 - MN
Could not find bond parameter for: NA - MN
Could not find bond parameter for: O2 - MN
Could not find bond parameter for: O2 - MN
Could not find bond parameter for: O - MN
Could not find bond parameter for: NA - MN
Could not find bond parameter for: NB - MN
Could not find bond parameter for: o - MN
Could not find bond parameter for: o - MN
Could not find bond parameter for: os - MN
Could not find bond parameter for: o - MN
Building angle parameters.
Could not find angle parameter: O2 - MN - os
Could not find angle parameter: O2 - MN - o
Could not find angle parameter: O2 - MN - o
Could not find angle parameter: O2 - MN - NA
Could not find angle parameter: O2 - MN - O2
Could not find angle parameter: C - O2 - MN
Could not find angle parameter: CW - NA - MN
Could not find angle parameter: H - NA - MN
Could not find angle parameter: NA - MN - os
Could not find angle parameter: NA - MN - o
Could not find angle parameter: NA - MN - o
Could not find angle parameter: NA - MN - O2
Could not find angle parameter: CR - NA - MN
Could not find angle parameter: O2 - MN - os
Could not find angle parameter: O2 - MN - o
Could not find angle parameter: O2 - MN - o
Could not find angle parameter: O2 - MN - o
Could not find angle parameter: O2 - MN - NA
Could not find angle parameter: O2 - MN - NB
Could not find angle parameter: O2 - MN - O
Could not find angle parameter: C - O2 - MN
Could not find angle parameter: C - O2 - MN
Could not find angle parameter: O - MN - o
Could not find angle parameter: O - MN - NA
Could not find angle parameter: O - MN - NB
Could not find angle parameter: C - O - MN
Could not find angle parameter: CW - NA - MN
Could not find angle parameter: H - NA - MN
Could not find angle parameter: NA - MN - o
Could not find angle parameter: NA - MN - NB
Could not find angle parameter: CR - NA - MN
Could not find angle parameter: CR - NB - MN
Could not find angle parameter: NB - MN - o
Could not find angle parameter: CC - NB - MN
Could not find angle parameter: c - o - MN
Could not find angle parameter: c - o - MN
Could not find angle parameter: os - MN - o
Could not find angle parameter: c3 - os - MN
Could not find angle parameter: c3 - os - MN
Could not find angle parameter: o - MN - os
Could not find angle parameter: o - MN - o
Could not find angle parameter: c - o - MN
Could not find angle parameter: MN - o - MN
Could not find angle parameter: MN - O2 - MN
Building proper torsion parameters.
1-4: angle 1345 4922 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 4923 4924 duplicates bond ('triangular' bond) or angle ('square'
bond)
** No torsion terms for O2-MN-os-c3
** No torsion terms for O2-MN-os-c3
** No torsion terms for O2-MN-o-c
** No torsion terms for O2-MN-o-c
** No torsion terms for O2-MN-o-MN
** No torsion terms for O2-MN-NA-CR
** No torsion terms for O2-MN-NA-H
** No torsion terms for O2-MN-NA-CW
** No torsion terms for O2-MN-O2-C
** No torsion terms for O2-MN-O2-MN
** No torsion terms for O2-C-O2-MN
** No torsion terms for C-O2-MN-os
** No torsion terms for C-O2-MN-o
** No torsion terms for C-O2-MN-o
** No torsion terms for C-O2-MN-NA
** No torsion terms for C-O2-MN-O2
** No torsion terms for CT-C-O2-MN
** No torsion terms for CW-NA-MN-os
** No torsion terms for CW-NA-MN-o
** No torsion terms for CW-NA-MN-o
** No torsion terms for CW-NA-MN-O2
** No torsion terms for H-NA-MN-os
** No torsion terms for H-NA-MN-o
** No torsion terms for H-NA-MN-o
** No torsion terms for H-NA-MN-O2
** No torsion terms for NA-MN-os-c3
** No torsion terms for NA-MN-os-c3
** No torsion terms for NA-MN-o-c
** No torsion terms for NA-MN-o-c
** No torsion terms for NA-MN-o-MN
** No torsion terms for NA-MN-O2-C
** No torsion terms for NA-MN-O2-MN
** No torsion terms for CR-NA-MN-os
** No torsion terms for CR-NA-MN-o
** No torsion terms for CR-NA-MN-o
** No torsion terms for CR-NA-MN-O2
** No torsion terms for O2-MN-os-c3
** No torsion terms for O2-MN-os-c3
** No torsion terms for O2-MN-o-c
** No torsion terms for O2-MN-o-c
** No torsion terms for O2-MN-o-MN
** No torsion terms for O2-MN-o-c
** No torsion terms for O2-MN-o-MN
** No torsion terms for O2-MN-NA-CR
** No torsion terms for O2-MN-NA-H
** No torsion terms for O2-MN-NA-CW
** No torsion terms for O2-MN-NB-CC
** No torsion terms for O2-MN-NB-CR
** No torsion terms for O2-MN-O-C
** No torsion terms for O2-C-O2-MN
** No torsion terms for O2-C-O2-MN
** No torsion terms for C-O2-MN-os
** No torsion terms for C-O2-MN-o
** No torsion terms for C-O2-MN-o
** No torsion terms for C-O2-MN-o
** No torsion terms for C-O2-MN-NA
** No torsion terms for C-O2-MN-NB
** No torsion terms for C-O2-MN-O
** No torsion terms for CT-C-O2-MN
** No torsion terms for CT-C-O2-MN
** No torsion terms for O-MN-o-c
** No torsion terms for O-MN-o-MN
** No torsion terms for O-MN-O2-MN
** No torsion terms for O-MN-NA-CR
** No torsion terms for O-MN-NA-H
** No torsion terms for O-MN-NA-CW
** No torsion terms for O-MN-NB-CC
** No torsion terms for O-MN-NB-CR
** No torsion terms for C-O-MN-o
** No torsion terms for C-O-MN-NA
** No torsion terms for C-O-MN-NB
** No torsion terms for CW-NA-MN-o
** No torsion terms for CW-NA-MN-NB
** No torsion terms for H-NA-MN-o
** No torsion terms for H-NA-MN-NB
** No torsion terms for NA-MN-o-c
** No torsion terms for NA-MN-o-MN
** No torsion terms for NA-MN-O2-MN
** No torsion terms for NA-MN-NB-CC
** No torsion terms for NA-MN-NB-CR
** No torsion terms for CR-NA-MN-o
** No torsion terms for CR-NA-MN-NB
** No torsion terms for CR-NB-MN-o
** No torsion terms for NB-MN-o-c
** No torsion terms for NB-MN-o-MN
** No torsion terms for NB-MN-O2-MN
** No torsion terms for CC-NB-MN-o
** No torsion terms for o-MN-O2-MN
** No torsion terms for o-MN-O2-MN
** No torsion terms for o-c-o-MN
** No torsion terms for o-c-o-MN
** No torsion terms for os-MN-o-c
** No torsion terms for os-MN-o-MN
** No torsion terms for os-MN-O2-MN
** No torsion terms for c3-os-MN-o
** No torsion terms for c3-os-MN-o
** No torsion terms for o-MN-os-c3
** No torsion terms for o-MN-os-c3
** No torsion terms for o-MN-o-c
** No torsion terms for o-MN-o-MN
** No torsion terms for o-MN-O2-MN
** No torsion terms for o-c-o-MN
** No torsion terms for c-o-MN-os
** No torsion terms for c-o-MN-o
** No torsion terms for c3-c-o-MN
** No torsion terms for c3-c-o-MN
** No torsion terms for c3-c-o-MN
Building improper torsion parameters.
total 1048 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
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Received on Tue Nov 08 2011 - 06:30:03 PST
