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
>
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Received on Tue Apr 05 2011 - 09:30:03 PDT
