Re: [AMBER] Non zero ligand warning

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Mon, 1 Feb 2021 00:41:24 +0800

Dear Prof,
I prepared the library file again with the index array as HPR. it was
accepted somehow by tleap when the complex was loaded.
Thank you
Regards

On Mon, Feb 1, 2021 at 12:12 AM Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:

> 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
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Sun Jan 31 2021 - 09:00:02 PST
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