[AMBER] About Mn2+ parameters in amber

From: Áõ¼ªÔª <liujiyuan.nwsuaf.edu.cn>
Date: Mon, 7 Nov 2011 12:14:48 +0800

   Dear everybody,
        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.
   ----------------------------------------------------------
> 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.
   -----------------------------------------------
   But when I runed 'saveamberparm complex ca-pp2a.prmtop ca-pp2a.inpcrd',I got
   serveral errors below,I thought that the metals.prp is not include the bond
   information,could you give me some advises,I need your help very much.
   ----------------------------------------------------------------------------
   --------
> 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.
   ---------------------------------------------------------------
   Best Regards

                          JiYuan Liu
   College of Plant Protection
   Northwest A&F University
   Yangling, Shaanxi
   China 712100
   Phone: 86-29-87092509
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Received on Sun Nov 06 2011 - 20:30:03 PST
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