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
>
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Received on Wed Feb 09 2011 - 09:30:02 PST
