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
>
>
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Received on Fri Nov 07 2014 - 07:00:03 PST
