Thanks ..yes this was the mistake.
I want to ask one more thing that the prm file in this case have exactly
same GLYCAM_06 parameters or not ? Is this editing of CT to CG id not
effecting the parms ?
On Tue, Apr 5, 2011 at 6:46 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> I just got it all to work. So... One possible answer... did you name
> the pdb file MFU and the prep file mfu? Residue names in leap are
> case sensitive.
>
>
> On Tue, Apr 5, 2011 at 12:20 PM, mish <smncbr.gmail.com> wrote:
> > I tried it in the way you mentioned before, but still there is some
> mistake
> > I am doing, which I can figure out.
> >
> > 1- tleap input file is :
> > source leaprc.GLYCAM_06
> > mfu = sequence { OME 0fA }
> > saveMol2 mfu mfu.mol2 1
> > quit
> >
> > 2- Edited residue name to MFU for whole residue and changed the residue
> > number to 1.
> >
> > 3- Then I ran the antechamber to get prep file :
> > antechamber -i mfu.mol2 -fi mol2 -o mfu.prep -fo prepi -at amber
> >
> > 4- Changed atomtype CT to CG in mfu.prep
> >
> > 5 - loading a pdb file of sequence { OME 0fA } with residue name MFU and
> > same residue number 1 for all atoms in tleap by file
> >
> > source leaprc.GLYCAM_06
> > loadamberprep mfu.prep
> > mefuc=loadpdb mfu.pdb
> > saveamberparm mfeuc mefuc.top mefuc.rst
> > quit
> >
> > I am getting the fallowing error :
> > -----------------------------
> >
> -----------------------------------------------------------------------------------------------------------------------------------
> >
> > Loading Prep file: ./mfu.prep
> > Loading PDB file: ./mfu.pdb
> > Added missing heavy atom: .R<MFU 1>.A<C2 23>
> > Added missing heavy atom: .R<MFU 1>.A<C3 19>
> > Added missing heavy atom: .R<MFU 1>.A<O2 25>
> > Added missing heavy atom: .R<MFU 1>.A<C1 6>
> > Added missing heavy atom: .R<MFU 1>.A<C4 15>
> > Added missing heavy atom: .R<MFU 1>.A<O3 21>
> > Added missing heavy atom: .R<MFU 1>.A<O5 8>
> > Added missing heavy atom: .R<MFU 1>.A<C5 9>
> > Added missing heavy atom: .R<MFU 1>.A<O4 17>
> > Added missing heavy atom: .R<MFU 1>.A<C6 11>
> > ERROR: Comparing atoms
> > .R<MFU 1>.A<O2 25>,
> > .R<MFU 1>.A<H2 2>,
> > .R<MFU 1>.A<H3 3>, and
> > .R<MFU 1>.A<H1 4>
> > to atoms
> > .R<MFU 1>.A<O 5>,
> > .R<MFU 1>.A<O2 25>,
> > .R<MFU 1>.A<H1 4>, and
> > .R<MFU 1>.A<H2 2>
> > This error may be due to faulty Connection atoms.
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [chirality.c], line 140
> > !FATAL: Message: Atom named O from MFU did not match !
> > !
> > !ABORTING.
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> > On Wed, Feb 9, 2011 at 6:39 PM, Lachele Foley (Lists) <lf.list.gmail.com
> >wrote:
> >
> >> Sorry... missed a bit.
> >>
> >> You need to change the CT atom types to CG in the prep file. I'm sure
> >> there's some way to instruct antechamber to do that for you, but
> >> changing the file is easy.
> >>
> >> It might not hurt, but it will probably be safer to change your
> >> residue name to something not already used in GLYCAM. So, make it FUC
> >> or ALF or whatever rather than ROH.
> >>
> >> I just tested with the following input (with the residue renamed ALF),
> >> and it worked:
> >>
> >> # if sleap for use in amber11: set default write14scale on
> >> source leaprc.GLYCAM_06
> >> loadamberprep ALF.prep
> >> saveamberparm ALF ALF.top ALF.rst
> >> quit
> >>
> >> If you load a pdb, just make sure the residue names match the new prep
> >> file.
> >>
> >>
> >> On Wed, Feb 9, 2011 at 12:18 PM, mish <smncbr.gmail.com> wrote:
> >> > Thanks a lot. I fallowed the same procedure for alpha-L-fucose (ROH
> and
> >> > 0fA). made a prepi file by antechamber and then loaded it in tleap.
> Then
> >> I
> >> > changed the residue name of one pdb file of alpha-L-fucose to ROH and
> >> loaded
> >> > this one too. Now if I check the unit it says that their are missing
> >> angle
> >> > parametres.
> >> >
> >>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >> >> a=loadpdb alfuc.pdb
> >> > Loading PDB file: ./alfuc.pdb
> >> > total atoms in file: 23
> >> >> check a
> >> > Checking 'a'....
> >> > Checking parameters for unit 'a'.
> >> > Checking for bond parameters.
> >> > Checking for angle parameters.
> >> > Could not find angle parameter: H1 - CT - OH
> >> > Could not find angle parameter: CT - OH - HO
> >> > Could not find angle parameter: OH - CT - CT
> >> > Could not find angle parameter: H1 - CT - OH
> >> > Could not find angle parameter: H1 - CT - CT
> >> > Could not find angle parameter: CT - OH - HO
> >> > Could not find angle parameter: CT - CT - H1
> >> > Could not find angle parameter: CT - CT - OH
> >> > Could not find angle parameter: OH - CT - CT
> >> > Could not find angle parameter: H1 - CT - OH
> >> > Could not find angle parameter: H1 - CT - CT
> >> > Could not find angle parameter: CT - OH - HO
> >> > Could not find angle parameter: CT - CT - H1
> >> > Could not find angle parameter: CT - CT - OH
> >> > Could not find angle parameter: CT - CT - CT
> >> > Could not find angle parameter: HC - CT - HC
> >> > Could not find angle parameter: HC - CT - HC
> >> > Could not find angle parameter: HC - CT - HC
> >> > Could not find angle parameter: CT - CT - CT
> >> > Could not find angle parameter: H1 - CT - CT
> >> > Could not find angle parameter: H1 - CT - CT
> >> > Could not find angle parameter: CT - CT - HC
> >> > Could not find angle parameter: CT - CT - HC
> >> > Could not find angle parameter: CT - CT - HC
> >> > Could not find angle parameter: CT - CT - H1
> >> > Could not find angle parameter: CT - CT - OH
> >> > Could not find angle parameter: CT - CT - CT
> >> > Could not find angle parameter: OS - CT - CT
> >> > Could not find angle parameter: OS - CT - H1
> >> > Could not find angle parameter: OS - CT - CT
> >> > Could not find angle parameter: OS - CT - CT
> >> > Could not find angle parameter: H2 - CT - OS
> >> > Could not find angle parameter: H2 - CT - CT
> >> > Could not find angle parameter: CT - OS - CT
> >> > Could not find angle parameter: CT - CT - CT
> >> > Could not find angle parameter: CT - CT - H1
> >> > Could not find angle parameter: CT - CT - OH
> >> > Could not find angle parameter: HO - OH - CT
> >> > Could not find angle parameter: OH - CT - H2
> >> > Could not find angle parameter: OH - CT - OS
> >> > Could not find angle parameter: OH - CT - CT
> >> > There are missing parameters.
> >> > Unit is OK.
> >> >
> >>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >> >
> >> > What could be the reason for it ?
> >> >
> >> > On Wed, Feb 9, 2011 at 5:08 PM, Lachele Foley (Lists) <
> lf.list.gmail.com
> >> >wrote:
> >> >
> >> >> I don't know of a way to do it in leap, but you can use a mol2 (use
> >> >> option 1 in [x|t]leap) made by leap as input for antechamber. Using
> >> >> antechamber, you can make a new prep-file that contains the entire
> >> >> molecule. Then, load that prep file into leap and build the prmtop
> >> >> from there. You might want to alter the residue name in the new prep
> >> >> file.
> >> >>
> >> >> x- or t- leap.input.file looks like:
> >> >> source leaprc.GLYCAM_06
> >> >> m = sequence { ROH 0GA }
> >> >> saveMol2 m m.mol2 1
> >> >> quit
> >> >>
> >> >> for sleap, use similar:
> >> >> set default write14scale on
> >> >> source leaprc.GLYCAM_06
> >> >> m = sequence { ROH 0GA }
> >> >> saveMol2 m m.mol2
> >> >> quit
> >> >>
> >> >> run leap:
> >> >> [x|t|s]leap -f leap.input.file
> >> >>
> >> >> run antechamber:
> >> >> antechamber -i m.mol2 -fi mol2 -o m.prep -fo prepi -at amber
> >> >>
> >> >> If anyone knows a better way to do it, please say.
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Feb 9, 2011 at 10:30 AM, mish <smncbr.gmail.com> wrote:
> >> >> > Hi all:
> >> >> > I have a problem with residue names of GLYCAM force field. I am
> using
> >> >> this
> >> >> > force field for FEP calculation. Since I am trying to prepare,
> >> minimize
> >> >> and
> >> >> > equilibrate the system using GLYCAM force field in AMBER and
> afterword
> >> I
> >> >> > will jump to something else. My problem is I need same (only one)
> >> residue
> >> >> > name for sugar molecules. In glycam it uses a different residue
> name
> >> for
> >> >> > ring atoms and for -OH group or -OCH3 group. Like for the
> >> transformation
> >> >> of
> >> >> > the molecule from me-alpla-L-fucoside (OME for -OCH3 and ofA for
> >> fucose
> >> >> > ring) to alpha-L-fucoside (ROH for -OH and 0fA for fucose ring) I
> want
> >> >> the
> >> >> > amber parameter files having same ATOM names. I found it difficult
> to
> >> >> edit
> >> >> > the topology file.
> >> >> >
> >> >> > Is it possible for leap to read the PBD file with proper amber
> naming
> >> >> > convention and then edit the atom/residue names, to make them same,
> in
> >> >> leap
> >> >> > and write the parameter file ?
> >> >> > or where can we try to change it in written parameter file ?
> >> >> >
> >> >> > Sincerely
> >> >> > mish
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> :-) Lachele
> >> >> Lachele Foley
> >> >> CCRC/UGA
> >> >> Athens, GA USA
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
> >> 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
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 10:30:03 PDT
