AMBER Archive (2007)

Subject: AMBER: Problem with LEaP generating topology and coord files after double bond creation

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Wed Nov 21 2007 - 14:45:17 CST

Hello Ambers,

I am trying to generate the input files for a simulation where the
structure has a double bond between a carbon on a substrate atom
and a nitrogen on the protein => a protonated Schiff base
(reaction goes by way of an imine intermediate). I have the
residue definition files and force field modifications for the
substrate and modified amino acids; there is no problem with that
part as far as I can tell, although antechamber's choice of atom
types looks "strange" to me. Using GAFF was not obviously better,
although I was going to explore that as a next step. LEaP also
created an entirely bogus bond that I had to delete.

I am including the LEaP script and the key part of the log file.
I think it hangs generating the topology because the bond created
is a double bond.

Any help appreciated.
Bud Dodson 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

log started: Wed Nov 21 14:24:35 2007

Log file: ./PIT-PIP.leap.log
>
> source leaprc.ff99SB
----- Source: /usr/local/share/amber9/dat/leap/cmd/leaprc.ff99SB
----- Source of /usr/local/share/amber9/dat/leap/cmd/leaprc.ff99SB done
>> logFile leap.log
log started: Wed Nov 21 14:24:35 2007

Log file: ./PIT-PIP.leap.log
>
> loadOff "./PIT.lib"
Loading library: ./PIT.lib
Loading: PIT
> loadOff "./PIP.lib"
Loading library: ./PIP.lib
Loading: PIP
> ABASIC = loadAmberParams "params.frcmod"
Loading parameters: ./params.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
>
> TheSeq = {
> PIT ARG ILE ASN LEU THR LEU VAL SER GLU LEU ALA ASP GLN HIS LEU
> MET ALA GLU TYR ARG GLU LEU PRO ARG VAL PHE GLY ALA VAL ARG LYS
> HID VAL ALA ASN GLY LYS ARG VAL ARG ASP PHE LYS ILE SER PRO THR
> PHE ILE LEU GLY ALA GLY HID VAL THR PHE PHE TYR ASP LYS LEU GLU
> PHE LEU ARG LYS ARG GLN ILE GLU LEU ILE ALA GLU CYS LEU LYS ARG
> GLY PHE ASN ILE LYS ASP THR THR VAL GLN ASP ILE SER ASP ILE PRO
> GLN GLU PHE ARG GLY ASP TYR ILE PRO HIE GLU ALA SER ILE ALA ILE
> SER GLN ALA ARG LEU ASP GLU LYS ILE ALA GLN ARG PRO THR TRP TYR
> LYS TYR TYR GLY LYS ALA ILE TYR CALA
> DC5 DC DA DG DG DA PIP DG DA DA DG DC DC3
> DG5 DG DC DT DT DC DA DT DC DC DT DG DG3 }
> THEPROT = loadPdbUsingSeq "2FCC_simulation.pdb" TheSeq
Loading PDB file: ./2FCC_simulation.pdb using sequence TheSeq
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
  matching pdb residues -> sequence template
        res pdb template
        1* THR PIT
        2 ARG ARG
        3 ILE ILE
        4 ASN ASN
        5 LEU LEU
        6 THR THR
        7 LEU LEU
        8 VAL VAL
        9 SER SER
        10 GLU GLU
        11 LEU LEU
        12 ALA ALA
        13 ASP ASP
        14 GLN GLN
        15* HIS HIE
        16 LEU LEU
        17 MET MET
        18 ALA ALA
        19 GLU GLU
        20 TYR TYR
        21 ARG ARG
        22 GLU GLU
        23 LEU LEU
        24 PRO PRO
        25 ARG ARG
        26 VAL VAL
        27 PHE PHE
        28 GLY GLY
        29 ALA ALA
        30 VAL VAL
        31 ARG ARG
        32 LYS LYS
        33* HIS HID
        34 VAL VAL
        35 ALA ALA
        36 ASN ASN
        37 GLY GLY
        38 LYS LYS
        39 ARG ARG
        40 VAL VAL
        41 ARG ARG
        42 ASP ASP
        43 PHE PHE
        44 LYS LYS
        45 ILE ILE
        46 SER SER
        47 PRO PRO
        48 THR THR
        49 PHE PHE
        50 ILE ILE
        51 LEU LEU
        52 GLY GLY
        53 ALA ALA
        54 GLY GLY
        55* HIS HID
        56 VAL VAL
        57 THR THR
        58 PHE PHE
        59 PHE PHE
        60 TYR TYR
        61 ASP ASP
        62 LYS LYS
        63 LEU LEU
        64 GLU GLU
        65 PHE PHE
        66 LEU LEU
        67 ARG ARG
        68 LYS LYS
        69 ARG ARG
        70 GLN GLN
        71 ILE ILE
        72 GLU GLU
        73 LEU LEU
        74 ILE ILE
        75 ALA ALA
        76 GLU GLU
        77 CYS CYS
        78 LEU LEU
        79 LYS LYS
        80 ARG ARG
        81 GLY GLY
        82 PHE PHE
        83 ASN ASN
        84 ILE ILE
        85 LYS LYS
        86 ASP ASP
        87 THR THR
        88 THR THR
        89 VAL VAL
        90 GLN GLN
        91 ASP ASP
        92 ILE ILE
        93 SER SER
        94 ASP ASP
        95 ILE ILE
        96 PRO PRO
        97 GLN GLN
        98 GLU GLU
        99 PHE PHE
        100 ARG ARG
        101 GLY GLY
        102 ASP ASP
        103 TYR TYR
        104 ILE ILE
        105 PRO PRO
        106* HIS HIE
        107 GLU GLU
        108 ALA ALA
        109 SER SER
        110 ILE ILE
        111 ALA ALA
        112 ILE ILE
        113 SER SER
        114 GLN GLN
        115 ALA ALA
        116 ARG ARG
        117 LEU LEU
        118 ASP ASP
        119 GLU GLU
        120 LYS LYS
        121 ILE ILE
        122 ALA ALA
        123 GLN GLN
        124 ARG ARG
        125 PRO PRO
        126 THR THR
        127 TRP TRP
        128 TYR TYR
        129 LYS LYS
        130 TYR TYR
        131 TYR TYR
        132 GLY GLY
        133 LYS LYS
        134 ALA ALA
        135 ILE ILE
        136 TYR TYR
        137 ALA CALA
        138 DC DC5
        139 DC DC
        140 DA DA
        141 DG DG
        142 DG DG
        143 DA DA
        144* PED PIP
        145 DG DG
        146 DA DA
        147 DA DA
        148 DG DG
        149 DC DC
        150 DC DC3
        151 DG DG5
        152 DG DG
        153 DC DC
        154 DT DT
        155 DT DT
        156 DC DC
        157 DA DA
        158 DT DT
        159 DC DC
        160 DC DC
        161 DT DT
        162 DG DG
        163 DG DG3
  * = possible mismatch; total 6
      (i.e. pdb name not a substring of template)

Joining PIT - ARG
Joining ARG - ILE
Joining ILE - ASN
Joining ASN - LEU
Joining LEU - THR
Joining THR - LEU
Joining LEU - VAL
Joining VAL - SER
Joining SER - GLU
Joining GLU - LEU
Joining LEU - ALA
Joining ALA - ASP
Joining ASP - GLN
Joining GLN - HIE
Joining HIE - LEU
Joining LEU - MET
Joining MET - ALA
Joining ALA - GLU
Joining GLU - TYR
Joining TYR - ARG
Joining ARG - GLU
Joining GLU - LEU
Joining LEU - PRO
Joining PRO - ARG
Joining ARG - VAL
Joining VAL - PHE
Joining PHE - GLY
Joining GLY - ALA
Joining ALA - VAL
Joining VAL - ARG
Joining ARG - LYS
Joining LYS - HID
Joining HID - VAL
Joining VAL - ALA
Joining ALA - ASN
Joining ASN - GLY
Joining GLY - LYS
Joining LYS - ARG
Joining ARG - VAL
Joining VAL - ARG
Joining ARG - ASP
Joining ASP - PHE
Joining PHE - LYS
Joining LYS - ILE
Joining ILE - SER
Joining SER - PRO
Joining PRO - THR
Joining THR - PHE
Joining PHE - ILE
Joining ILE - LEU
Joining LEU - GLY
Joining GLY - ALA
Joining ALA - GLY
Joining GLY - HID
Joining HID - VAL
Joining VAL - THR
Joining THR - PHE
Joining PHE - PHE
Joining PHE - TYR
Joining TYR - ASP
Joining ASP - LYS
Joining LYS - LEU
Joining LEU - GLU
Joining GLU - PHE
Joining PHE - LEU
Joining LEU - ARG
Joining ARG - LYS
Joining LYS - ARG
Joining ARG - GLN
Joining GLN - ILE
Joining ILE - GLU
Joining GLU - LEU
Joining LEU - ILE
Joining ILE - ALA
Joining ALA - GLU
Joining GLU - CYS
Joining CYS - LEU
Joining LEU - LYS
Joining LYS - ARG
Joining ARG - GLY
Joining GLY - PHE
Joining PHE - ASN
Joining ASN - ILE
Joining ILE - LYS
Joining LYS - ASP
Joining ASP - THR
Joining THR - THR
Joining THR - VAL
Joining VAL - GLN
Joining GLN - ASP
Joining ASP - ILE
Joining ILE - SER
Joining SER - ASP
Joining ASP - ILE
Joining ILE - PRO
Joining PRO - GLN
Joining GLN - GLU
Joining GLU - PHE
Joining PHE - ARG
Joining ARG - GLY
Joining GLY - ASP
Joining ASP - TYR
Joining TYR - ILE
Joining ILE - PRO
Joining PRO - HIE
Joining HIE - GLU
Joining GLU - ALA
Joining ALA - SER
Joining SER - ILE
Joining ILE - ALA
Joining ALA - ILE
Joining ILE - SER
Joining SER - GLN
Joining GLN - ALA
Joining ALA - ARG
Joining ARG - LEU
Joining LEU - ASP
Joining ASP - GLU
Joining GLU - LYS
Joining LYS - ILE
Joining ILE - ALA
Joining ALA - GLN
Joining GLN - ARG
Joining ARG - PRO
Joining PRO - THR
Joining THR - TRP
Joining TRP - TYR
Joining TYR - LYS
Joining LYS - TYR
Joining TYR - TYR
Joining TYR - GLY
Joining GLY - LYS
Joining LYS - ALA
Joining ALA - ILE
Joining ILE - TYR
Joining TYR - CALA
Joining DC5 - DC
Joining DC - DA
Joining DA - DG
Joining DG - DG
Joining DG - DA
Joining DA - PIP
Joining PIP - DG
Joining DG - DA
Joining DA - DA
Joining DA - DG
Joining DG - DC
Joining DC - DC3
Joining DG5 - DG
Joining DG - DC
Joining DC - DT
  Added missing heavy atom: .R<DT 155>.A<C7 17>
Joining DT - DT
  Added missing heavy atom: .R<DT 156>.A<C7 17>
Joining DT - DC
Joining DC - DA
Joining DA - DT
  Added missing heavy atom: .R<DT 159>.A<C7 17>
Joining DT - DC
Joining DC - DC
Joining DC - DT
  Added missing heavy atom: .R<DT 162>.A<C7 17>
Joining DT - DG
Joining DG - DG3
  total atoms in file: 1643
  Leap added 1437 missing atoms according to residue templates:
       4 Heavy
       1433 H / lone pairs
>
> # Add bond command here to create double bond between PIP.C1* and PIT.N
> bond THEPROT.2.1 THEPROT.145.17 "D"
> desc THEPROT.2.1
ATOM
             Normal Perturbed
Name: N N
Type: N* N*
Charge: 0.0433 0.000
Polarization: 0.0000 0.000
Element: N (not affected by pert)
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: -7.432000, 141.115000, 29.873000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<PIT 2>.A<H1 2> by a single bond.
  Bonded to .R<PIT 2>.A<CA 3> by a single bond.
  Bonded to .R<PIP 145>.A<C1* 17> by a double bond.
> desc THEPROT.145.17
ATOM
             Normal Perturbed
Name: C1* C1*
Type: CM CM
Charge: 0.1496 0.000
Polarization: 0.0000 0.000
Element: C (not affected by pert)
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: -8.620000, 141.322000, 28.995000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<PIP 145>.A<C2* 14> by a single bond.
  Bonded to .R<PIP 145>.A<H1*1 18> by a single bond.
  Bonded to .R<PIP 145>.A<O3* 19> by a single bond.
  Bonded to .R<PIT 2>.A<N 1> by a double bond.
> deleteBond THEPROT.145.17 THEPROT.145.19
> desc THEPROT.145.17
ATOM
             Normal Perturbed
Name: C1* C1*
Type: CM CM
Charge: 0.1496 0.000
Polarization: 0.0000 0.000
Element: C (not affected by pert)
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: -8.620000, 141.322000, 28.995000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<PIP 145>.A<C2* 14> by a single bond.
  Bonded to .R<PIP 145>.A<H1*1 18> by a single bond.
  Bonded to .R<PIT 2>.A<N 1> by a double bond.
>
> SavePDB THEPROT "vac.pdb"
Writing pdb file: vac.pdb
 Converting C-terminal residue name to PDB format: CALA -> ALA
> SaveAmberParm THEPROT "vac.prmtop" "vac.inpcrd"
Checking Unit.
WARNING: The unperturbed charge of the unit: -19.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for H-CT-N*-CM
        atoms are: H1 CA N C1*
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 total 615 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
<program hangs here, using 100% CPU>

logfile "PIT-PIP.leap.log"

source leaprc.ff99SB
logfile "PIT-PIP.leap.log"

loadOff "./PIT.lib"
loadOff "./PIP.lib"
ABASIC = loadAmberParams "params.frcmod"

TheSeq = {
PIT ARG ILE ASN LEU THR LEU VAL SER GLU LEU ALA ASP GLN HIS LEU
MET ALA GLU TYR ARG GLU LEU PRO ARG VAL PHE GLY ALA VAL ARG LYS
HID VAL ALA ASN GLY LYS ARG VAL ARG ASP PHE LYS ILE SER PRO THR
PHE ILE LEU GLY ALA GLY HID VAL THR PHE PHE TYR ASP LYS LEU GLU
PHE LEU ARG LYS ARG GLN ILE GLU LEU ILE ALA GLU CYS LEU LYS ARG
GLY PHE ASN ILE LYS ASP THR THR VAL GLN ASP ILE SER ASP ILE PRO
GLN GLU PHE ARG GLY ASP TYR ILE PRO HIE GLU ALA SER ILE ALA ILE
SER GLN ALA ARG LEU ASP GLU LYS ILE ALA GLN ARG PRO THR TRP TYR
LYS TYR TYR GLY LYS ALA ILE TYR CALA
DC5 DC DA DG DG DA PIP DG DA DA DG DC DC3
DG5 DG DC DT DT DC DA DT DC DC DT DG DG3 }
THEPROT = loadPdbUsingSeq "2FCC_simulation.pdb" TheSeq

# Add bond command here to create double bond between PIP.C1* and PIT.N
bond THEPROT.2.1 THEPROT.145.17 "D"
desc THEPROT.2.1
desc THEPROT.145.17
deleteBond THEPROT.145.17 THEPROT.145.19
desc THEPROT.145.17

SavePDB THEPROT "vac.pdb"
SaveAmberParm THEPROT "vac.prmtop" "vac.inpcrd"
quit

THEPROT_sol = Copy THEPROT
SolvateOct THEPROT_sol TIP3PBOX 10.0
SavePDB THEPROT_sol "wat.pdb"
SaveAmberParm THEPROT_sol "wat.prmtop" "wat.inpcrd"

THEPROT_cio = Copy THEPROT_sol
AddIons THEPROT_cio Na+ 0
SavePDB THEPROT_cio "cio.pdb"
SaveAmberParm THEPROT_cio "cio.prmtop" "cio.inpcrd"

quit

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