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

From: mish <smncbr.gmail.com>
Date: Wed, 9 Feb 2011 16:30:02 +0100

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 ?

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Received on Wed Feb 09 2011 - 08:00:04 PST
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