Dear Shivangi,
This is a common mistake . Don't worry. Before solving this you have to
understand the basics of error.
Step 1: Once you loaded *.leaprc file in xleap/sleap/tleap, it will
automatically look for the files embedded in the bottom line of the *leaprc.
parm* = loadamberparams parm*.dat
frcmod*SB = loadamberparams frcmod.ff*SB
loadOff amino*.lib
Now these files are responsible for the exact matching between your atom
types (in pdb file) and the template atom type in forcefield.
Step 2: If any of the atom type is not matching then it will throw error of
"*missing atom*", This is where your problem lies.
Step 3: In order to change the atom types according to templates you have
to open **amino*.in* files what you will find in your
*$AMBERHOME/dat/leap/prep* folder, and change the atom types which are not
matching.
I hope this will solve your problem
thanks and regrads
Santanu Santra
On Tue, Jul 9, 2019 at 6:41 PM shivangi agarwal <
shiviagarwalpharma.gmail.com> wrote:
> Thanks, loaded source.leaprc.protein.ff14SB, recognized residues but showe
> error as
> > com=loadpdb complex.pdb
> Loading PDB file: ./complex_42_noH_no_HOH_2.pdb
> (starting new molecule for chain )
> -- residue 512: duplicate [ C] atoms (total 21)
> -- residue 512: duplicate [ N] atoms (total 5)
> -- residue 512: duplicate [ O] atoms (total 4)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Added missing heavy atom: .R<GLU 165>.A<CG 8>
> Added missing heavy atom: .R<GLU 165>.A<CD 11>
> Added missing heavy atom: .R<GLU 165>.A<OE1 12>
> Added missing heavy atom: .R<GLU 165>.A<OE2 13>
> Added missing heavy atom: .R<ASP 236>.A<CG 8>
> Added missing heavy atom: .R<ASP 236>.A<OD1 9>
> Added missing heavy atom: .R<ASP 236>.A<OD2 10>
> Created a new atom named: OXT within residue: .R<PRO 259>
> Added missing heavy atom: .R<GLU 416>.A<CG 8>
> Added missing heavy atom: .R<GLU 416>.A<CD 11>
> Added missing heavy atom: .R<GLU 416>.A<OE1 12>
> Added missing heavy atom: .R<GLU 416>.A<OE2 13>
> Added missing heavy atom: .R<ASP 487>.A<CG 8>
> Added missing heavy atom: .R<ASP 487>.A<OD1 9>
> Added missing heavy atom: .R<ASP 487>.A<OD2 10>
> Added missing heavy atom: .R<LIG 512>.A<N4 26>
> Added missing heavy atom: .R<LIG 512>.A<C18 23>
> Added missing heavy atom: .R<LIG 512>.A<O1 28>
> Added missing heavy atom: .R<LIG 512>.A<C17 22>
> Added missing heavy atom: .R<LIG 512>.A<C19 24>
> Added missing heavy atom: .R<LIG 512>.A<C16 21>
> Added missing heavy atom: .R<LIG 512>.A<C20 25>
> Added missing heavy atom: .R<LIG 512>.A<C15 20>
> Added missing heavy atom: .R<LIG 512>.A<N3 19>
> Added missing heavy atom: .R<LIG 512>.A<C14 18>
> Added missing heavy atom: .R<LIG 512>.A<N2 17>
> Added missing heavy atom: .R<LIG 512>.A<O2 29>
> Added missing heavy atom: .R<LIG 512>.A<C6 7>
> Added missing heavy atom: .R<LIG 512>.A<C7 9>
> Added missing heavy atom: .R<LIG 512>.A<C4 5>
> Added missing heavy atom: .R<LIG 512>.A<O3 30>
> Added missing heavy atom: .R<LIG 512>.A<N1 10>
> Added missing heavy atom: .R<LIG 512>.A<C8 11>
> Added missing heavy atom: .R<LIG 512>.A<C3 4>
> Added missing heavy atom: .R<LIG 512>.A<C5 6>
> Added missing heavy atom: .R<LIG 512>.A<C9 12>
> Added missing heavy atom: .R<LIG 512>.A<C13 16>
> Added missing heavy atom: .R<LIG 512>.A<C2 3>
> Added missing heavy atom: .R<LIG 512>.A<C10 13>
> Added missing heavy atom: .R<LIG 512>.A<C12 15>
> Added missing heavy atom: .R<LIG 512>.A<C1 2>
> Added missing heavy atom: .R<LIG 512>.A<C11 14>
> total atoms in file: 3913
> Leap added 3862 missing atoms according to residue templates:
> 41 Heavy
> 3821 H / lone pairs
> The file contained 1 atoms not in residue templates
> > saveAmberParm com see.inpcrd see.prmtop
> Checking Unit.
>
> Warning: There is a bond of 40.101967 angstroms between:
>
> Warning: There is a bond of 14.630144 angstroms between:
>
> Warning: There is a bond of 8.520137 angstroms between:
>
> Warning: There is a bond of 6.768709 angstroms between:
>
> Warning: The unperturbed charge of the unit (-14.001000) is not zero.
> *FATAL: Atom .R<PRO 259>.A<OXT 15> does not have a type.*
>
> Error: Failed to generate parameters
>
> Warning: Parameter file was not saved.
>
> On Tue, Jul 9, 2019 at 6:28 PM Santanu Santra <santop420.gmail.com> wrote:
>
> > Dear Shivangi,
> >
> > I guess you forgot to load corresponding leaprc file for protein .
> Because
> > once you have loaded leaprc file for protein it will recognize all the
> > amino acid rresidues. Hope this will work. Thanks and Regards.
> > Santanu Santra
> >
> > On Tue, Jul 9, 2019 at 6:23 PM shivangi agarwal <
> > shiviagarwalpharma.gmail.com> wrote:
> >
> > > Thanks for your reply.
> > >
> > > I have installed AmberTools19. When I am loading my protein
> > _ligand_complex
> > > file (complex loadpdb complex.pdb), it is showing error.
> > > I am hereby attaching error message and complex.pdb
> > > Kindly suggest.
> > >
> > > On Tue, Jul 9, 2019 at 10:26 AM somdev pahari <somdevpahari1.gmail.com
> >
> > > wrote:
> > >
> > > > Dear Shivangi,
> > > >
> > > > Yes, you can install AmberTools 19 with Amber12. Here I paste a
> > link.
> > > >
> > http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
> > > > Hope it will help you.
> > > >
> > > > Regards
> > > > Somdev Pahari
> > > > PhD Scholar
> > > > NIT Rourkela
> > > > India
> > > >
> > > > On Tue, Jul 9, 2019 at 9:40 AM shivangi agarwal <
> > > > shiviagarwalpharma.gmail.com> wrote:
> > > >
> > > > > I have downloaded AmberTools 19. Will the same license key work for
> > > > > AmberTools 19 as for Amber12?.
> > > > >
> > > > >
> > > > >
> > > > > Regards
> > > > > Shivangi
> > > > >
> > > > > On Mon, Jul 8, 2019 at 6:58 PM Daniel Roe <daniel.r.roe.gmail.com>
> > > > wrote:
> > > > >
> > > > > > On Mon, Jul 8, 2019 at 3:41 AM shivangi agarwal
> > > > > > <shiviagarwalpharma.gmail.com> wrote:
> > > > > > >
> > > > > > > Hereby, i am attaching my terminal commands which I have given.
> > > > > > > Please go through the commands and suggest me a possible
> solution
> > > to
> > > > > come
> > > > > > > out of this error.
> > > > > >
> > > > > > Did you follow the advice previously given to you and try
> > AmberTools
> > > > > > 19, read chapter 3, etc? Your output still shows you as using
> Amber
> > > > > > 12, which is extremely out of date. It also shows a warning at
> the
> > > > > > very beginning (about assigned bond types being wrong). Have you
> > > > > > attempted to look into this? How did you generate ligand2.pdb?
> > > > > >
> > > > > > The tutorial you are following is categorized as advanced. I
> highly
> > > > > > recommend that you try to complete some of the basic tutorials
> > first
> > > > > > so you can get a better feel for what antechamber/leap are trying
> > to
> > > > > > do, which in turn will give you the tools to better troubleshoot
> > > these
> > > > > > issues.
> > > > > >
> > > > > > -Dan
> > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Thanks and regards
> > > > > > > Shivangi Agarwal
> > > > > > >
> > > > > > > On Wed, Jul 3, 2019 at 11:15 PM David Case <
> > david.case.rutgers.edu
> > > >
> > > > > > wrote:
> > > > > > >
> > > > > > > > On Wed, Jul 03, 2019, shivangi agarwal wrote:
> > > > > > > >
> > > > > > > > > For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+
> > > > > > > > >
> > > > > > > > >*antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2
> -c
> > > bcc
> > > > -s
> > > > > > > > >2parmchk -i ligand.mol2 -f mol2 -o ligand.frcmodtleapsource
> > > > > > > > >leaprc.ff99SBsource leaprc.gaffLIG=loadmol2
> > ligand.mol2listcheck
> > > > > > > > >LIGloadamberparams ligand.frcmodsaveoff LIG
> > > > ligand.libsaveamberparm
> > > > > > LIG
> > > > > > > > >ligand.prmtop ligand.inpcrdquittleap -s -f Zn.intleapsource
> > > > > > > > >leaprc.ff99SBsource leaprc.gaffloadamberparams
> > > > ligand.frcmodloadoff
> > > > > > > > >atomic_ions.libloadoff ligand.libcomplex =loadpdb
> > > > > > rec_lig.pdbsaveamberparm
> > > > > > > > >complex rec_lig.prmtop rec_lig.inpcrdsavepdb complex
> > > rec_lig.pdb*
> > > > > > > >
> > > > > > > > Your email program (or maybe mine?) has made it very hard to
> > read
> > > > the
> > > > > > > > above. But it looks like you are using a very old version of
> > > > > > > > AmberTools, since we have not had a "leaprc.ff99SB" in the
> > search
> > > > > path
> > > > > > > > for many years. I suspect that you are never loading the
> > > > parameters
> > > > > > for
> > > > > > > > ions like zinc.
> > > > > > > >
> > > > > > > > I think you are going to have to download AmberTools19, and
> > read
> > > > > > Chapter
> > > > > > > > 3 about how force fields are loaded. You can keep your old
> > > > ligand.*
> > > > > > > > files. The default approach will treat interactions between
> > zinc
> > > > and
> > > > > > > > other atoms as non-bonded ones. You'll have to see if this
> > meets
> > > > > your
> > > > > > > > needs. If not, consult sections 15.7 and 15.8 in the manual,
> > > which
> > > > > > > > discusses ways to handle metals.
> > > > > > > >
> > > > > > > > ...good luck....dac
> > > > > > > >
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
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> > > > > > > >
> > > > > > > _______________________________________________
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> > > > > >
> > > > > > _______________________________________________
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> > > > > >
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> > > > >
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> > >
> >
> >
> > --
> > Santanu Santra
> > Research Scholar
> > Molecular Simulation Laboratory
> > Department of Chemistry
> > NIT ROURKELA
> > ROURKELA, 769008
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Santanu Santra
Research Scholar
Molecular Simulation Laboratory
Department of Chemistry
NIT ROURKELA
ROURKELA, 769008
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Received on Tue Jul 09 2019 - 07:00:02 PDT
