Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)

From: Lachele Foley (Lists) <"Lachele>
Date: Wed, 9 Feb 2011 11:08:57 -0500

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

x- or t- leap.input.file looks like:
    source leaprc.GLYCAM_06
    m = sequence { ROH 0GA }
    saveMol2 m m.mol2 1

for sleap, use similar:
    set default write14scale on
    source leaprc.GLYCAM_06
    m = sequence { ROH 0GA }
    saveMol2 m m.mol2

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 <> 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

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Wed Feb 09 2011 - 08:30:04 PST
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