On Thu, Sep 26, 2019, Patil Pranita Uttamrao wrote:
>I am trying to prepare the residue library and force field parameters of
>the modified residue G7M(.cif attached) using antechamber as given below.
>
>$ antechamber -fi ccif -i G7M.cif -bk G7M -fo ac -o G7M.ac -c bcc -at amber
Pulling a block from components.cif generally won't work for modified
residues (just for non-covalent ligands.) The PDB add hydrogens to make
all components neutral -- this is generally not what you want, so
hand-editing of these files is usually needed.
See
http://ambermd.org/tutorials/basic/tutorial5/index.htm for basic
instructions on preparing a modified residue: you need to add capping
groups, do the quantum charge calculation, then remove the capping
groups.
Note also that starting parameters for 7-methyl-guanosine are already
available for Amber: see the all_modrna08.lib and related files.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 28 2019 - 06:00:04 PDT
