Tried doing with mol2 file also but same error.
> a= loadpdb pdb1_10854218DOCK.pdb
Loading PDB file: ./pdb1_10854218DOCK.pdb
Created a new atom named: OXT within residue: .R<CYS 212>
ERROR: Comparing atoms
.R<CYS 212>.A<C 10>,
.R<DRG 1>.A<H 2>,
.R<DRG 1>.A<H1 3>, and
.R<DRG 1>.A<H2 4>
to atoms
.R<DRG 1>.A<C1 5>,
.R<CYS 212>.A<C 10>,
.R<DRG 1>.A<H2 4>, and
.R<DRG 1>.A<H 2>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C1 from DRG did not match !
!
!ABORTING.
Thanks for helping.
Best regards,
Ruchika
On Fri, Nov 7, 2014 at 9:52 AM, Wei Ye <yw20055968.126.com> wrote:
> First, make sure the file to make prepin and frcmod are correct. I
> recommend using MOL2 file format to do anetchamber.
> Then, when you do tleap, delete all the CONECT information in the complex
> pdb. This information has been stored in prepin file.
> And make sure all the atom names are correct in the complex pdb with
> prepin file.
>
>
> HTH,
> Wei.
> 在2014年11月07 22时47分, "Ruchika Bhat"<ruchikabhat31.gmail.com>写道:
>
> *This is the error it is showing :*
>
> > source leaprc.gaff
> ----- Source: /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc.gaff
> ----- Source of /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc.gaff
> done
> Log file: ./leap.log
> Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end (June,
> 2003)
> > loadamberprep ligand1DRG.prepin
> Loading Prep file: ./ligand1DRG.prepin
> > loadamberparams ligand1drg.frcmod
> Loading parameters: ./ligand1drg.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> > a = loadpdb pdb1_10854218DOCK.pdb
> Loading PDB file: ./pdb1_10854218DOCK.pdb
> Created a new atom named: OXT within residue: .R<CYS 212>
> ERROR: Comparing atoms
> .R<CYS 212>.A<C 10>,
> .R<DRG 1>.A<H 2>,
> .R<DRG 1>.A<H1 3>, and
> .R<DRG 1>.A<H2 4>
> to atoms
> .R<DRG 1>.A<C1 5>,
> .R<CYS 212>.A<C 10>,
> .R<DRG 1>.A<H2 4>, and
> .R<DRG 1>.A<H 2>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 140
> !FATAL: Message: Atom named C1 from DRG did not match !
> !
> !ABORTING.
>
> On Fri, Nov 7, 2014 at 8:08 PM, Gulsevin,Alican <agulsevin.ufl.edu> wrote:
>
> > It can be several things. Your ligand has atoms AMBER does not
> > recognize, check the frcmod file for sometimes antechamber is not able
> > to recognize particular atoms and generates void parameters, which are
> > not recognized later by tleap. Also, you need to load the frcmod file
> > before you read the pdb, I don't know if that's the problem because you
> > don't have your leap script here, but checking it can be useful as well.
> >
> > Alican
> >
> > On Fri, 7 Nov 2014 19:09:07 +0530, Ruchika Bhat wrote:
> > > ?Hi everyone,
> > >
> > > Please guide me what is the command to generate the top and crd file
> > > once I
> > > generated the frcmod and prepin files.
> > >
> > > In the command
> > >> saveamberparm DRG ligand.prmtop ligand.inpcrd
> > >
> > > The DRG = loadpdb pdb1_10854218DOCK.pdb
> > >
> > > But when I load the DRG with the protein ligand complex it is giving:
> > >
> > >
> > > Loading PDB file: ./pdb1_10854218DOCK.pdb
> > > Unknown residue: DRG number: 212 type: Terminal/last
> > > ..relaxing end constraints to try for a dbase match
> > > -no luck
> > > Created a new atom named: OXT within residue: .R<CYS 212>
> > > Creating new UNIT for residue: DRG sequence: 213
> > > One sided connection. Residue: missing connect0 atom.
> > > Created a new atom named: C within residue: .R<DRG 213>
> > > Created a new atom named: H within residue: .R<DRG 213>
> > > Created a new atom named: H1 within residue: .R<DRG 213>
> > > Created a new atom named: H2 within residue: .R<DRG 213>
> > > Created a new atom named: C1 within residue: .R<DRG 213>
> > > Created a new atom named: H3 within residue: .R<DRG 213>
> > > Created a new atom named: H4 within residue: .R<DRG 213>
> > > Created a new atom named: O within residue: .R<DRG 213>
> > > Created a new atom named: C2 within residue: .R<DRG 213>
> > > Created a new atom named: O1 within residue: .R<DRG 213>
> > > Created a new atom named: C3 within residue: .R<DRG 213>
> > > Created a new atom named: C29 within residue: .R<DRG 213>
> > > Created a new atom named: N3 within residue: .R<DRG 213>
> > > Created a new atom named: C4 within residue: .R<DRG 213>
> > > Created a new atom named: H5 within residue: .R<DRG 213>
> > > Created a new atom named: C5 within residue: .R<DRG 213>
> > > Created a new atom named: C10 within residue: .R<DRG 213>
> > > Created a new atom named: C9 within residue: .R<DRG 213>
> > > Created a new atom named: H8 within residue: .R<DRG 213>
> > > Created a new atom named: H9 within residue: .R<DRG 213>
> > > Created a new atom named: C6 within residue: .R<DRG 213>
> > > Created a new atom named: H6 within residue: .R<DRG 213>
> > > Created a new atom named: C7 within residue: .R<DRG 213>
> > > Created a new atom named: H7 within residue: .R<DRG 213>
> > > Created a new atom named: C8 within residue: .R<DRG 213>
> > > Created a new atom named: N within residue: .R<DRG 213>
> > > Created a new atom named: C14 within residue: .R<DRG 213>
> > > Created a new atom named: C13 within residue: .R<DRG 213>
> > > Created a new atom named: H14 within residue: .R<DRG 213>
> > > Created a new atom named: H15 within residue: .R<DRG 213>
> > > Created a new atom named: H16 within residue: .R<DRG 213>
> > > Created a new atom named: H17 within residue: .R<DRG 213>
> > > Created a new atom named: C11 within residue: .R<DRG 213>
> > > Created a new atom named: H10 within residue: .R<DRG 213>
> > > Created a new atom named: H11 within residue: .R<DRG 213>
> > > Created a new atom named: C12 within residue: .R<DRG 213>
> > > Created a new atom named: H12 within residue: .R<DRG 213>
> > > Created a new atom named: H13 within residue: .R<DRG 213>
> > > Created a new atom named: N1 within residue: .R<DRG 213>
> > > Created a new atom named: C15 within residue: .R<DRG 213>
> > > Created a new atom named: H18 within residue: .R<DRG 213>
> > > Created a new atom named: H19 within residue: .R<DRG 213>
> > > Created a new atom named: C16 within residue: .R<DRG 213>
> > > Created a new atom named: H20 within residue: .R<DRG 213>
> > > Created a new atom named: H21 within residue: .R<DRG 213>
> > > Created a new atom named: N2 within residue: .R<DRG 213>
> > > Created a new atom named: C28 within residue: .R<DRG 213>
> > > Created a new atom named: O3 within residue: .R<DRG 213>
> > > Created a new atom named: C17 within residue: .R<DRG 213>
> > > Created a new atom named: O2 within residue: .R<DRG 213>
> > > Created a new atom named: C18 within residue: .R<DRG 213>
> > > Created a new atom named: C19 within residue: .R<DRG 213>
> > > Created a new atom named: H22 within residue: .R<DRG 213>
> > > Created a new atom named: C20 within residue: .R<DRG 213>
> > > Created a new atom named: H23 within residue: .R<DRG 213>
> > > Created a new atom named: C21 within residue: .R<DRG 213>
> > > Created a new atom named: H24 within residue: .R<DRG 213>
> > > Created a new atom named: C22 within residue: .R<DRG 213>
> > > Created a new atom named: C23 within residue: .R<DRG 213>
> > > Created a new atom named: C24 within residue: .R<DRG 213>
> > > Created a new atom named: C25 within residue: .R<DRG 213>
> > > Created a new atom named: H25 within residue: .R<DRG 213>
> > > Created a new atom named: C26 within residue: .R<DRG 213>
> > > Created a new atom named: H26 within residue: .R<DRG 213>
> > > Created a new atom named: C27 within residue: .R<DRG 213>
> > > Created a new atom named: H27 within residue: .R<DRG 213>
> > > total atoms in file: 3493
> > > The file contained 67 atoms not in residue templates
> > >
> > >
> > > *Please help me with how to proceed with making top and crd files,
> > > after I
> > > generated the prepin and frcmod files.*
> > >
> > > Thanking for your valuable time and guidance.
> > >
> > > Best Regards,
> > > Ruchika
> > > _______________________________________________
> > > 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
Received on Fri Nov 07 2014 - 10:30:02 PST
