Dear Santanu sir
Thanks for your reply. Actually when I am saving the pdb complex using
tleap, my complex ligand connections getting changed and the ligand seems
to be broken. This may be due to wrong connections written by tleap
program. However, when I am generating ligand.mol2 using antechamber -i
ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2, it is generated
correctly as my input file "ligand.pdb". Kindly suggest.
Kindly look into the attached files and suggest.
Also, the error which was previously coming for OR<PRO 259>.A<OXT 15> atom
has gone now without doing any changes in any file.
Thanks and regards
On Tue, Jul 9, 2019 at 7:00 PM Santanu Santra <santop420.gmail.com> wrote:
> 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
> > > > > > > > > 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
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> 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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: commands
Received on Wed Jul 10 2019 - 00:30:02 PDT
