Dear Prof.
Thank you. I somehow managed to solve the issue by loading the ions frcmod
file first and then loading the ligand file.
Now there is another issue which I am not sure why it is coming as my order
of preparing the files for simulation is the same.
Amber is giving the error of creating new atom for ligand although the
frcmod file and library file are loaded before loading the complex. I am
pasting my leap log. I could not spot the error. Checked the name of the
molecule in the ligand library too. but it looks correct.
------------------------------------------------------------------------------------------------
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: /mnt/d/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: /mnt/d/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: /mnt/d/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: /mnt/d/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: /mnt/d/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.gaff2
----- Source: /mnt/d/amber18/dat/leap/cmd/leaprc.gaff2
----- Source of /mnt/d/amber18/dat/leap/cmd/leaprc.gaff2 done
>> logFile leap.log
log started: Sun Jan 31 23:44:46 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" }
>> { "op" "O" "sp3" }
>> { "oq" "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" }
>> { "cs" "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" }
>> { "n7" "N" "sp3" }
>> { "n8" "N" "sp3" }
>> { "n9" "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" }
>> { "ns" "N" "sp2" }
>> { "nt" "N" "sp2" }
>> { "nu" "N" "sp2" }
>> { "nv" "N" "sp2" }
>> { "nx" "N" "sp3" }
>> { "ny" "N" "sp3" }
>> { "nz" "N" "sp3" }
>> { "n+" "N" "sp3" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "sp" "S" "sp3" }
>> { "sq" "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 gaff2.dat
Loading parameters: /mnt/d/amber18/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
(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: n5)
(UNKNOWN ATOM TYPE: n6)
>
> source leaprc.water.tip3p
----- Source: /mnt/d/amber18/dat/leap/cmd/leaprc.water.tip3p
----- Source of /mnt/d/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: /mnt/d/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: /mnt/d/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: /mnt/d/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: /mnt/d/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: /mnt/d/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)
>>
>
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /mnt/d/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)
> set default PBRadii mbondi3
Using ArgH and AspGluO modified Bondi2 radii
> loadamberparams lig.frcmod
Loading parameters: ./lig.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadoff lig.lib
Loading library: ./lig.lib
Loading: lig
> complex = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
(starting new molecule for chain A)
Matching PDB residue names to LEaP variables.
Warning: Unknown residue: HPR number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Mapped residue PRO, term: Terminal/beginning, seq. number: 1 to: NPRO.
Mapped residue PRO, term: Terminal/last, seq. number: 321 to: CPRO.
Creating new UNIT for residue: HPR sequence: 1
Created a new atom named: O1 within residue: .R<HPR 1>
Created a new atom named: C13 within residue: .R<HPR 1>
Created a new atom named: C14 within residue: .R<HPR 1>
Created a new atom named: C15 within residue: .R<HPR 1>
Created a new atom named: C16 within residue: .R<HPR 1>
Created a new atom named: C17 within residue: .R<HPR 1>
Created a new atom named: O2 within residue: .R<HPR 1>
Created a new atom named: C19 within residue: .R<HPR 1>
Created a new atom named: C21 within residue: .R<HPR 1>
Created a new atom named: O8 within residue: .R<HPR 1>
Created a new atom named: C22 within residue: .R<HPR 1>
Created a new atom named: C25 within residue: .R<HPR 1>
Created a new atom named: C23 within residue: .R<HPR 1>
Created a new atom named: C29 within residue: .R<HPR 1>
------------------------------------------------------------------------------------
The lig.lib entry
!entry.lig.unit.name single str
"HPR"
------------------------------------------
Attaching the complex file also.
Thank you once again
Regards
On Sun, Jan 31, 2021 at 10:25 PM David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Jan 31, 2021, Ayesha Fatima wrote:
>
> >I have a protein-ligand system. For the ligand, i calculated the RESP
> >charges using the Pyred server. Then i prepared my files for simulation.
> >when I developed the ligand prmtop, amber gave a warning of 0.1239
> >unperturbed charge. How do i neutralise this?
>
> First, check the RED/RESP charges for your ligand: do they add up to
> 0.1239?
> Is the ligand supposed to be neutral? If the problem turns out to be the
> RESP charges, you will need to make changes at that step.
>
> I can't help with that, but maybe R.E.D. users on the list can chime in, if
> they have seen any similar kind of behavior. If the problem is not with
> the
> RESP charges, then we will need to know more details about how you prepared
> the ligand prmtop file.
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 31 2021 - 08:30:02 PST
