AMBER Archive (2003)

Subject: AMBER: leap/frcmod problem

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Wed Sep 17 2003 - 15:08:37 CDT

Hi -

I'm preparing the prmtop file for a protein-peptide complex with
non-standard residues (phospho-Tyr, modified Asp and Glu). I prepare a
frcmod file for the modifid force field (new bond, angle, dihedral, etc.
parameters), but tleap doesn't recognize the bond parameters. I can't see
anything obviously wrong in the frcmod file. Any idea as to where thoings
go wrong?

Thanks in advance.

Joseph

-------------------------------------------------------------------
frcmod.pty1
--------------------------------------------------------------------

MASS
HH 10.08 hydroxyl group in protonated ASD,GLD (JN)
BOND
C -OS 320.0 1.290 PHOSPHOTYROSINE
OH-HH 999.0 1.000 hydroxyl group in protonated ASD,GLD (JN)

ANGLE
CA-C -OS 35.0 124.71 PHOSPHOTYROSINE
C -OS-P 100. 126.00 PHOSPHOTYROSINE
C -OH-HH 100.0 113.00
CT-OH-HH 100.0 108.50

DIHE
X -C -OS-X 2 1.800 180.000 2.000

NONBON
  HH 0.6000 0.0157

-----------------------------------------------------------------------
leapht.in
-----------------------------------------------------------------------
frcmod = loadamberparams frcmod.pty1
loadamberprep pty1.in
loadamberprep arn.in
loadamberprep asd.in
loadamberprep gld.in
set PTY restype undefined
set ARN restype undefined
set ASD restype undefined
set GLD restype undefined
1spshm = loadpdb 1spsd.pdb
saveamberparm 1spshm 1spshm.top 1spshm.crd

------------------------------------------------------------------------
leap.log
-----------------------------------------------------------------------
log started: Wed Sep 17 16:21:33 2003

Log file: ./leap.log
.
.
.
(deleted)
.
.
.
> source leapht.in
----- Source: ./leapht.in
----- Source of ./leapht.in done
>> frcmod = loadamberparams frcmod.pty1
Loading parameters: ./frcmod.pty1
Reading force field mod type file (frcmod)
ERROR: BOND: mass not read - omitting
ERROR: C: mass not read - omitting
(UNKNOWN ATOM TYPE: HH)
>> loadamberprep pty1.in
Loading Prep file: ./pty1.in
Loaded UNIT: PTY
>> loadamberprep arn.in
Loading Prep file: ./arn.in
Loaded UNIT: ARN
>> loadamberprep asd.in
Loading Prep file: ./asd.in
(UNKNOWN ATOM TYPE: HH)
Loaded UNIT: ASD
>> loadamberprep gld.in
Loading Prep file: ./gld.in
(UNKNOWN ATOM TYPE: HH)
Loaded UNIT: GLD
>> set PTY restype undefined
>> set ARN restype undefined
>> set ASD restype undefined
>> set GLD restype undefined
>> 1spshm = loadpdb 1spsd.pdb
Loading PDB file: ./1spsd.pdb
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
(Residue 1: GLD, Nonterminal, was not found in name map.)
(Residue 2: GLD, Nonterminal, was not found in name map.)
(Residue 3: TRP, Nonterminal, was not found in name map.)
(Residue 4: TYR, Nonterminal, was not found in name map.)
(Residue 5: PHE, Nonterminal, was not found in name map.)
(Residue 6: GLY, Nonterminal, was not found in name map.)
(Residue 7: LYN, Nonterminal, was not found in name map.)
(Residue 8: ILE, Nonterminal, was not found in name map.)
(Residue 9: THR, Nonterminal, was not found in name map.)
(Residue 10: ARG, Nonterminal, was not found in name map.)
(Residue 11: ARN, Nonterminal, was not found in name map.)
(Residue 12: GLD, Nonterminal, was not found in name map.)
(Residue 13: SER, Nonterminal, was not found in name map.)
(Residue 14: GLD, Nonterminal, was not found in name map.)
(Residue 15: ARN, Nonterminal, was not found in name map.)
(Residue 16: LEU, Nonterminal, was not found in name map.)
(Residue 17: LEU, Nonterminal, was not found in name map.)
(Residue 18: LEU, Nonterminal, was not found in name map.)
(Residue 19: ASN, Nonterminal, was not found in name map.)
(Residue 20: PRO, Nonterminal, was not found in name map.)
(Residue 21: GLD, Nonterminal, was not found in name map.)
(Residue 22: ASN, Nonterminal, was not found in name map.)
(Residue 23: PRO, Nonterminal, was not found in name map.)
(Residue 24: ARN, Nonterminal, was not found in name map.)
(Residue 25: GLY, Nonterminal, was not found in name map.)
(Residue 26: THR, Nonterminal, was not found in name map.)
(Residue 27: PHE, Nonterminal, was not found in name map.)
(Residue 28: LEU, Nonterminal, was not found in name map.)
(Residue 29: VAL, Nonterminal, was not found in name map.)
(Residue 30: ARG, Nonterminal, was not found in name map.)
(Residue 31: GLD, Nonterminal, was not found in name map.)
(Residue 32: SER, Nonterminal, was not found in name map.)
(Residue 33: GLD, Nonterminal, was not found in name map.)
(Residue 34: THR, Nonterminal, was not found in name map.)
(Residue 35: THR, Nonterminal, was not found in name map.)
(Residue 36: LYN, Nonterminal, was not found in name map.)
(Residue 37: GLY, Nonterminal, was not found in name map.)
(Residue 38: ALA, Nonterminal, was not found in name map.)
(Residue 39: TYR, Nonterminal, was not found in name map.)
(Residue 40: CYS, Nonterminal, was not found in name map.)
(Residue 41: LEU, Nonterminal, was not found in name map.)
(Residue 42: SER, Nonterminal, was not found in name map.)
(Residue 43: VAL, Nonterminal, was not found in name map.)
(Residue 44: SER, Nonterminal, was not found in name map.)
(Residue 45: ASD, Nonterminal, was not found in name map.)
(Residue 46: PHE, Nonterminal, was not found in name map.)
(Residue 47: ASD, Nonterminal, was not found in name map.)
(Residue 48: ASN, Nonterminal, was not found in name map.)
(Residue 49: ALA, Nonterminal, was not found in name map.)
(Residue 50: LYN, Nonterminal, was not found in name map.)
(Residue 51: GLY, Nonterminal, was not found in name map.)
(Residue 52: LEU, Nonterminal, was not found in name map.)
(Residue 53: ASN, Nonterminal, was not found in name map.)
(Residue 54: VAL, Nonterminal, was not found in name map.)
(Residue 55: LYN, Nonterminal, was not found in name map.)
(Residue 56: HIS, Nonterminal, was not found in name map.)
(Residue 57: TYR, Nonterminal, was not found in name map.)
(Residue 58: LYN, Nonterminal, was not found in name map.)
(Residue 59: ILE, Nonterminal, was not found in name map.)
(Residue 60: ARN, Nonterminal, was not found in name map.)
(Residue 61: LYN, Nonterminal, was not found in name map.)
(Residue 62: LEU, Nonterminal, was not found in name map.)
(Residue 63: ASD, Nonterminal, was not found in name map.)
(Residue 64: SER, Nonterminal, was not found in name map.)
(Residue 65: GLY, Nonterminal, was not found in name map.)
(Residue 66: GLY, Nonterminal, was not found in name map.)
(Residue 67: PHE, Nonterminal, was not found in name map.)
(Residue 68: TYR, Nonterminal, was not found in name map.)
(Residue 69: ILE, Nonterminal, was not found in name map.)
(Residue 70: THR, Nonterminal, was not found in name map.)
(Residue 71: SER, Nonterminal, was not found in name map.)
(Residue 72: ARN, Nonterminal, was not found in name map.)
(Residue 73: THR, Nonterminal, was not found in name map.)
(Residue 74: GLN, Nonterminal, was not found in name map.)
(Residue 75: PHE, Nonterminal, was not found in name map.)
(Residue 76: SER, Nonterminal, was not found in name map.)
(Residue 77: SER, Nonterminal, was not found in name map.)
(Residue 78: LEU, Nonterminal, was not found in name map.)
(Residue 79: GLN, Nonterminal, was not found in name map.)
(Residue 80: GLN, Nonterminal, was not found in name map.)
(Residue 81: LEU, Nonterminal, was not found in name map.)
(Residue 82: VAL, Nonterminal, was not found in name map.)
(Residue 83: ALA, Nonterminal, was not found in name map.)
(Residue 84: TYR, Nonterminal, was not found in name map.)
(Residue 85: TYR, Nonterminal, was not found in name map.)
(Residue 86: SER, Nonterminal, was not found in name map.)
(Residue 87: LYN, Nonterminal, was not found in name map.)
(Residue 88: HIS, Nonterminal, was not found in name map.)
(Residue 89: ALA, Nonterminal, was not found in name map.)
(Residue 90: ASD, Nonterminal, was not found in name map.)
(Residue 91: GLY, Nonterminal, was not found in name map.)
(Residue 92: LEU, Nonterminal, was not found in name map.)
(Residue 93: CYS, Nonterminal, was not found in name map.)
(Residue 94: HIS, Nonterminal, was not found in name map.)
(Residue 95: ARN, Nonterminal, was not found in name map.)
(Residue 96: LEU, Nonterminal, was not found in name map.)
(Residue 97: THR, Nonterminal, was not found in name map.)
(Residue 98: ASN, Nonterminal, was not found in name map.)
(Residue 99: VAL, Nonterminal, was not found in name map.)
(Residue 100: CYS, Nonterminal, was not found in name map.)
(Residue 101: PRO, Nonterminal, was not found in name map.)
Mapped residue THR, term: Terminal/last, seq. number: 102 to: CTHR.
Mapped residue PRO, term: Terminal/beginning, seq. number: 103 to: NPRO.
(Residue 104: GLN, Nonterminal, was not found in name map.)
(Residue 105: PTY, Nonterminal, was not found in name map.)
(Residue 106: GLD, Nonterminal, was not found in name map.)
(Residue 107: GLD, Nonterminal, was not found in name map.)
(Residue 108: ILE, Nonterminal, was not found in name map.)
Mapped residue PRO, term: Terminal/last, seq. number: 109 to: CPRO.
Joining NALA - GLD
Joining GLD - GLD
Joining GLD - TRP
Joining TRP - TYR
Joining TYR - PHE
Joining PHE - GLY
Joining GLY - LYN
Joining LYN - ILE
Joining ILE - THR
Joining THR - ARG
Joining ARG - ARN
Joining ARN - GLD
Joining GLD - SER
Joining SER - GLD
Joining GLD - ARN
Joining ARN - LEU
Joining LEU - LEU
Joining LEU - LEU
Joining LEU - ASN
Joining ASN - PRO
Joining PRO - GLD
Joining GLD - ASN
Joining ASN - PRO
Joining PRO - ARN
Joining ARN - GLY
Joining GLY - THR
Joining THR - PHE
Joining PHE - LEU
Joining LEU - VAL
Joining VAL - ARG
Joining ARG - GLD
Joining GLD - SER
Joining SER - GLD
Joining GLD - THR
Joining THR - THR
Joining THR - LYN
Joining LYN - GLY
Joining GLY - ALA
Joining ALA - TYR
Joining TYR - CYS
Joining CYS - LEU
Joining LEU - SER
Joining SER - VAL
Joining VAL - SER
Joining SER - ASD
Joining ASD - PHE
Joining PHE - ASD
Joining ASD - ASN
Joining ASN - ALA
Joining ALA - LYN
Joining LYN - GLY
Joining GLY - LEU
Joining LEU - ASN
Joining ASN - VAL
Joining VAL - LYN
Joining LYN - HID
Joining HID - TYR
Joining TYR - LYN
Joining LYN - ILE
Joining ILE - ARN
Joining ARN - LYN
Joining LYN - LEU
Joining LEU - ASD
Joining ASD - SER
Joining SER - GLY
Joining GLY - GLY
Joining GLY - PHE
Joining PHE - TYR
Joining TYR - ILE
Joining ILE - THR
Joining THR - SER
Joining SER - ARN
Joining ARN - THR
Joining THR - GLN
Joining GLN - PHE
Joining PHE - SER
Joining SER - SER
Joining SER - LEU
Joining LEU - GLN
Joining GLN - GLN
Joining GLN - LEU
Joining LEU - VAL
Joining VAL - ALA
Joining ALA - TYR
Joining TYR - TYR
Joining TYR - SER
Joining SER - LYN
Joining LYN - HID
Joining HID - ALA
Joining ALA - ASD
Joining ASD - GLY
Joining GLY - LEU
Joining LEU - CYS
Joining CYS - HID
Joining HID - ARN
Joining ARN - LEU
Joining LEU - THR
Joining THR - ASN
Joining ASN - VAL
Joining VAL - CYS
Joining CYS - PRO
Joining PRO - CTHR
Joining NPRO - GLN
  Added missing heavy atom: .R<GLN 10106>.A<CG 8>
  Added missing heavy atom: .R<GLN 10106>.A<CD 11>
  Added missing heavy atom: .R<GLN 10106>.A<OE1 12>
  Added missing heavy atom: .R<GLN 10106>.A<NE2 13>
Joining GLN - PTY
Joining PTY - GLD
Joining GLD - GLD
Joining GLD - ILE
Joining ILE - CPRO
  total atoms in file: 897
  Leap added 885 missing atoms according to residue templates:
       4 Heavy
       868 H / lone pairs
       13 unknown element
>> saveamberparm 1spshm 1spshm.top 1spshm.crd
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.030000 is not integral.
WARNING: The unperturbed charge of the unit: 0.030000 is not zero.

 -- ignoring the error and warning.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Could not find bond parameter for: C - OS
Could not find bond parameter for: OH - HH
Could not find bond parameter for: OH - HH
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <GLD 3>: -M CA N H
 <GLD 3>: CA +M C O
 <GLD 3>: CG OE1 CD OE2
 <GLD 4>: -M CA N H
 <GLD 4>: CA +M C O
 <GLD 4>: CG OE1 CD OE2
 <ARN 13>: -M CA N H
 <ARN 13>: CA +M C O
 <ARN 13>: NE NH1 CZ NH2
 <ARN 13>: CD CZ NE HE
 <ARN 13>: CZ HH11 NH1 HH12
 <ARN 13>: CZ HH21 NH2 HH22
 <GLD 14>: -M CA N H
 <GLD 14>: CA +M C O
 <GLD 14>: CG OE1 CD OE2
 <GLD 16>: -M CA N H
 <GLD 16>: CA +M C O
 <GLD 16>: CG OE1 CD OE2
 <ARN 17>: -M CA N H
 <ARN 17>: CA +M C O
 <ARN 17>: NE NH1 CZ NH2
 <ARN 17>: CD CZ NE HE
 <ARN 17>: CZ HH11 NH1 HH12
 <ARN 17>: CZ HH21 NH2 HH22
 <GLD 23>: -M CA N H
 <GLD 23>: CA +M C O
 <GLD 23>: CG OE1 CD OE2
 <ARN 26>: -M CA N H
 <ARN 26>: CA +M C O
 <ARN 26>: NE NH1 CZ NH2
 <ARN 26>: CD CZ NE HE
 <ARN 26>: CZ HH11 NH1 HH12
 <ARN 26>: CZ HH21 NH2 HH22
 <GLD 33>: -M CA N H
 <GLD 33>: CA +M C O
 <GLD 33>: CG OE1 CD OE2
 <GLD 35>: -M CA N H
 <GLD 35>: CA +M C O
 <GLD 35>: CG OE1 CD OE2
 <ASD 47>: -M CA N H
 <ASD 47>: CA +M C O
 <ASD 47>: CB OD1 CG OD2
 <ASD 49>: -M CA N H
 <ASD 49>: CA +M C O
 <ASD 49>: CB OD1 CG OD2
 <ARN 62>: -M CA N H
 <ARN 62>: CA +M C O
 <ARN 62>: NE NH1 CZ NH2
 <ARN 62>: CD CZ NE HE
 <ARN 62>: CZ HH11 NH1 HH12
 <ARN 62>: CZ HH21 NH2 HH22
 <ASD 65>: -M CA N H
 <ASD 65>: CA +M C O
 <ASD 65>: CB OD1 CG OD2
 <ARN 74>: -M CA N H
 <ARN 74>: CA +M C O
 <ARN 74>: NE NH1 CZ NH2
 <ARN 74>: CD CZ NE HE
 <ARN 74>: CZ HH11 NH1 HH12
 <ARN 74>: CZ HH21 NH2 HH22
 <ASD 92>: -M CA N H
 <ASD 92>: CA +M C O
 <ASD 92>: CB OD1 CG OD2
 <ARN 97>: -M CA N H
 <ARN 97>: CA +M C O
 <ARN 97>: NE NH1 CZ NH2
 <ARN 97>: CD CZ NE HE
 <ARN 97>: CZ HH11 NH1 HH12
 <ARN 97>: CZ HH21 NH2 HH22
 <PTY 10107>: -M CA N H
 <PTY 10107>: CA +M C O
 <PTY 10107>: CG CE2 CD2 HD2
 <PTY 10107>: CD2 CZ CE2 HE2
 <PTY 10107>: CD1 CZ CE1 HE1
 <PTY 10107>: CG CE1 CD1 HD1
 <PTY 10107>: CD1 CD2 CG CB
 <PTY 10107>: CE1 CE2 CZ OH
 <GLD 10108>: -M CA N H
 <GLD 10108>: CA +M C O
 <GLD 10108>: CG OE1 CD OE2
 <GLD 10109>: -M CA N H
 <GLD 10109>: CA +M C O
 <GLD 10109>: CG OE1 CD OE2
 total 371 improper torsions applied
 83 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
>>
>
> quit
        Quit 

-- 
--------------------------------------------------------------------
Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
--------------------------------------------------------------------

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