Dear Amber Users
I have a protein where I have a modified amino acid residue beta hydroxy
aspartic acid. It is written as BHD in our PDB file. I followed the
instructions on
https://ambermd.org/tutorials/basic/tutorial4b/index.php for
the BHD unit extracted from the original PDB file and managed to generate
the frcmod and lib files. I removed hydrogen atoms from the original PDB
file and ran Leap to add the hydrogen atoms back and also generate the top
and crd files. Files were generated. However, the output PDB file has a TER
cut before and after the modified residue, although the starting file did
not have it.
I ran a few steps of minimisation and equilibration and from the final
minimised rst file, when I used the ambpdb command to generate the pfb file
(ambpdb -p *.prmtop -c *.rst >.pdb, it returned errors :
Error: Atom 1015 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if
the
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for pz-bhd.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for pz-bhd.prmtop.
It did generate the output PDB file that apparently looked fine on
inspecting. However, it had the issue of the TER cut. I removed the TER
from the PDB file manually and tried to run Leap in a water box. It
returned this error:
log started: Wed Apr 21 19:56:58 2021
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "H" "H" "sp3" }
>> { "HO" "H" "sp3" }
>> { "HS" "H" "sp3" }
>> { "H1" "H" "sp3" }
>> { "H2" "H" "sp3" }
>> { "H3" "H" "sp3" }
>> { "H4" "H" "sp3" }
>> { "H5" "H" "sp3" }
>> { "HW" "H" "sp3" }
>> { "HC" "H" "sp3" }
>> { "HA" "H" "sp3" }
>> { "HP" "H" "sp3" }
>> { "HZ" "H" "sp3" }
>> { "OH" "O" "sp3" }
>> { "OS" "O" "sp3" }
>> { "O" "O" "sp2" }
>> { "O2" "O" "sp2" }
>> { "OP" "O" "sp2" }
>> { "OW" "O" "sp3" }
>> { "CT" "C" "sp3" }
>> { "CX" "C" "sp3" }
>> { "C8" "C" "sp3" }
>> { "2C" "C" "sp3" }
>> { "3C" "C" "sp3" }
>> { "CH" "C" "sp3" }
>> { "CS" "C" "sp2" }
>> { "C" "C" "sp2" }
>> { "CO" "C" "sp2" }
>> { "C*" "C" "sp2" }
>> { "CA" "C" "sp2" }
>> { "CB" "C" "sp2" }
>> { "CC" "C" "sp2" }
>> { "CN" "C" "sp2" }
>> { "CM" "C" "sp2" }
>> { "CK" "C" "sp2" }
>> { "CQ" "C" "sp2" }
>> { "CD" "C" "sp2" }
>> { "C5" "C" "sp2" }
>> { "C4" "C" "sp2" }
>> { "CP" "C" "sp2" }
>> { "CI" "C" "sp3" }
>> { "CJ" "C" "sp2" }
>> { "CW" "C" "sp2" }
>> { "CV" "C" "sp2" }
>> { "CR" "C" "sp2" }
>> { "CA" "C" "sp2" }
>> { "CY" "C" "sp2" }
>> { "C0" "Ca" "sp3" }
>> { "MG" "Mg" "sp3" }
>> { "N" "N" "sp2" }
>> { "NA" "N" "sp2" }
>> { "N2" "N" "sp2" }
>> { "N*" "N" "sp2" }
>> { "NP" "N" "sp2" }
>> { "NQ" "N" "sp2" }
>> { "NB" "N" "sp2" }
>> { "NC" "N" "sp2" }
>> { "NT" "N" "sp3" }
>> { "NY" "N" "sp2" }
>> { "N3" "N" "sp3" }
>> { "S" "S" "sp3" }
>> { "SH" "S" "sp3" }
>> { "P" "P" "sp3" }
>> { "LP" "" "sp3" }
>> { "EP" "" "sp3" }
>> { "F" "F" "sp3" }
>> { "Cl" "Cl" "sp3" }
>> { "Br" "Br" "sp3" }
>> { "I" "I" "sp3" }
>> }
>> #
>> # Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /home/suchetana/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /home/suchetana/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
>> #
>> # Load main chain and terminating amino acid libraries
>> #
>> loadOff amino12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>>
>> #
>> # Define the PDB name map for the amino acids
>> #
>> addPdbResMap {
>> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" }
>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>> }
>>
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>
> source leaprc.gaff
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Wed Apr 21 19:56:58 2021
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "cz" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pc" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "pe" "P" "sp3" }
>> { "pf" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/suchetana/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
(UNKNOWN ATOM TYPE: oq)
(UNKNOWN ATOM TYPE: ni)
(UNKNOWN ATOM TYPE: nj)
(UNKNOWN ATOM TYPE: nk)
(UNKNOWN ATOM TYPE: nl)
(UNKNOWN ATOM TYPE: nm)
(UNKNOWN ATOM TYPE: nn)
(UNKNOWN ATOM TYPE: sp)
(UNKNOWN ATOM TYPE: sq)
>
> loadoff atomic_ions.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
> loadamberparams bhd.frcmod
Loading parameters: ./bhd.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadoff bhd.lib
Loading library: ./bhd.lib
Loading: BHD
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters:
/home/suchetana/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> loadamberparams frcmod.ions234lm_126_tip3p
Loading parameters:
/home/suchetana/amber18/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
model (12-6 normal usage set)
(UNKNOWN ATOM TYPE: Be2+)
(UNKNOWN ATOM TYPE: Cu2+)
(UNKNOWN ATOM TYPE: Ni2+)
(UNKNOWN ATOM TYPE: Pt2+)
(UNKNOWN ATOM TYPE: Zn2+)
(UNKNOWN ATOM TYPE: Co2+)
(UNKNOWN ATOM TYPE: Pd2+)
(UNKNOWN ATOM TYPE: Ag2+)
(UNKNOWN ATOM TYPE: Cr2+)
(UNKNOWN ATOM TYPE: Fe2+)
(UNKNOWN ATOM TYPE: Mg2+)
(UNKNOWN ATOM TYPE: V2+)
(UNKNOWN ATOM TYPE: Mn2+)
(UNKNOWN ATOM TYPE: Hg2+)
(UNKNOWN ATOM TYPE: Cd2+)
(UNKNOWN ATOM TYPE: Yb2+)
(UNKNOWN ATOM TYPE: Ca2+)
(UNKNOWN ATOM TYPE: Sn2+)
(UNKNOWN ATOM TYPE: Pb2+)
(UNKNOWN ATOM TYPE: Eu2+)
(UNKNOWN ATOM TYPE: Sr2+)
(UNKNOWN ATOM TYPE: Sm2+)
(UNKNOWN ATOM TYPE: Ba2+)
(UNKNOWN ATOM TYPE: Ra2+)
(UNKNOWN ATOM TYPE: Al3+)
(UNKNOWN ATOM TYPE: Fe3+)
(UNKNOWN ATOM TYPE: Cr3+)
(UNKNOWN ATOM TYPE: In3+)
(UNKNOWN ATOM TYPE: Tl3+)
(UNKNOWN ATOM TYPE: Y3+)
(UNKNOWN ATOM TYPE: La3+)
(UNKNOWN ATOM TYPE: Ce3+)
(UNKNOWN ATOM TYPE: Pr3+)
(UNKNOWN ATOM TYPE: Nd3+)
(UNKNOWN ATOM TYPE: Sm3+)
(UNKNOWN ATOM TYPE: Eu3+)
(UNKNOWN ATOM TYPE: Gd3+)
(UNKNOWN ATOM TYPE: Tb3+)
(UNKNOWN ATOM TYPE: Dy3+)
(UNKNOWN ATOM TYPE: Er3+)
(UNKNOWN ATOM TYPE: Tm3+)
(UNKNOWN ATOM TYPE: Lu3+)
(UNKNOWN ATOM TYPE: Hf4+)
(UNKNOWN ATOM TYPE: Zr4+)
(UNKNOWN ATOM TYPE: Ce4+)
(UNKNOWN ATOM TYPE: U4+)
(UNKNOWN ATOM TYPE: Pu4+)
(UNKNOWN ATOM TYPE: Th4+)
> source leaprc.water.tip3p
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.water.tip3p done
>> #
>> # Load water and ions for TIP3P + Joung-Chetham monovalent ions
>> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set)
>> #
>> addAtomTypes {
>> { "HW" "H" "sp3" }
>> { "OW" "O" "sp3" }
>> { "F-" "F" "sp3" }
>> { "Cl-" "Cl" "sp3" }
>> { "Br-" "Br" "sp3" }
>> { "I-" "I" "sp3" }
>> { "Li+" "Li" "sp3" }
>> { "Na+" "Na" "sp3" }
>> { "K+" "K" "sp3" }
>> { "Rb+" "Rb" "sp3" }
>> { "Cs+" "Cs" "sp3" }
>> { "Mg+" "Mg" "sp3" }
>> { "Tl+" "Tl" "sp3" }
>> { "Cu+" "Cu" "sp3" }
>> { "Ag+" "Ag" "sp3" }
>> { "Be2+" "Be" "sp3" }
>> { "Cu2+" "Cu" "sp3" }
>> { "Ni2+" "Ni" "sp3" }
>> { "Pt2+" "Pt" "sp3" }
>> { "Zn2+" "Zn" "sp3" }
>> { "Co2+" "Co" "sp3" }
>> { "Pd2+" "Pd" "sp3" }
>> { "Ag2+" "Ag" "sp3" }
>> { "Cr2+" "Cr" "sp3" }
>> { "Fe2+" "Fe" "sp3" }
>> { "Mg2+" "Mg" "sp3" }
>> { "V2+" "V" "sp3" }
>> { "Mn2+" "Mn" "sp3" }
>> { "Hg2+" "Hg" "sp3" }
>> { "Cd2+" "Cd" "sp3" }
>> { "Yb2+" "Yb" "sp3" }
>> { "Ca2+" "Ca" "sp3" }
>> { "Sn2+" "Sn" "sp3" }
>> { "Pb2+" "Pb" "sp3" }
>> { "Eu2+" "Eu" "sp3" }
>> { "Sr2+" "Sr" "sp3" }
>> { "Sm2+" "Sm" "sp3" }
>> { "Ba2+" "Ba" "sp3" }
>> { "Ra2+" "Ra" "sp3" }
>> { "Al3+" "Al" "sp3" }
>> { "Fe3+" "Fe" "sp3" }
>> { "Cr3+" "Cr" "sp3" }
>> { "In3+" "In" "sp3" }
>> { "Tl3+" "Tl" "sp3" }
>> { "Y3+" "Y" "sp3" }
>> { "La3+" "La" "sp3" }
>> { "Ce3+" "Ce" "sp3" }
>> { "Pr3+" "Pr" "sp3" }
>> { "Nd3+" "Nd" "sp3" }
>> { "Sm3+" "Sm" "sp3" }
>> { "Eu3+" "Eu" "sp3" }
>> { "Gd3+" "Gd" "sp3" }
>> { "Tb3+" "Tb" "sp3" }
>> { "Dy3+" "Dy" "sp3" }
>> { "Er3+" "Er" "sp3" }
>> { "Tm3+" "Tm" "sp3" }
>> { "Lu3+" "Lu" "sp3" }
>> { "Hf4+" "Hf" "sp3" }
>> { "Zr4+" "Zr" "sp3" }
>> { "Ce4+" "Ce" "sp3" }
>> { "U4+" "U" "sp3" }
>> { "Pu4+" "Pu" "sp3" }
>> { "Th4+" "Th" "sp3" }
>> }
>> loadOff atomic_ions.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/atomic_ions.lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OP3
Loading: OPC
Loading: OPC3BOX
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>> loadAmberParams frcmod.tip3p
Loading parameters: /home/suchetana/amber18/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
>> loadAmberParams frcmod.ionsjc_tip3p
Loading parameters:
/home/suchetana/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip3p
Loading parameters:
/home/suchetana/amber18/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
model (12-6 normal usage set)
>>
>
> set default PBRadii mbondi3
Using ArgH and AspGluO modified Bondi2 radii
> loadAmberPrep cgu_new.prepin
Loading Prep file: ./cgu_new.prepin
Loaded UNIT: CGU
> loadAmberParams frcmod2.cgu
Loading parameters: ./frcmod2.cgu
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadAmberParams frcmod1.cgu
Loading parameters: ./frcmod1.cgu
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
>
> x = loadPDB min3-f.pdb
Loading PDB file: ./min3-f.pdb
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
Mapped residue ASN, term: Terminal/last, seq. number: 358 to: CASN.
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
Starting new chain with CA
total atoms in file: 5546
>
> bond x.18.SG x.23.SG
> bond x.56.SG x.71.SG
/home/suchetana/amber18/bin/teLeap: Fatal Error!
bond: Argument #2 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
I had also tried to do a fixatomorder before doing the ambpdb step. Even
with that output file, I got the same error.
Here is my input for that.
fixatomorder outprefix fixed
trajin min3.rst
trajout fixed.min3.rst7
run
quit
Would be grateful if you can suggest a fix for this.
Thanks
Suchetana Gupta
IACS, India
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Received on Wed Apr 21 2021 - 08:00:02 PDT
