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
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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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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>
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Received on Tue Jul 09 2019 - 06:30:02 PDT
