You can construct a new residue using prep file without xleap. The prep
file contains bond connectivity, atom type, charge, improper dihedral
information. Please see amber/dat/leap/prep/*.in for examples. If you can
find a similar residue in the standard prep files, you may copy/edit the
relevant part. After you create the file, you can use leap/xleap/gleap to
convert it to a lib/off file (see amber/dat/leap/lib/*.cmd for examples).
If you need to change/add bond/angle/dihedral/van der Waals parameters,
you may edit parmxx.dat or add a frcmod.xx (see
amber/dat/leap/parm/frcmod.* for examples). You also need to add the
associated bond/angle/dihedral/VDW parameters when you define a new atom
type.
yong
On 9/19/11 10:37 PM, "Yao Yao" <yao0o.ymail.com> wrote:
>Hi,
>
>I plan to transfer the amber ff parameters for a new residue in another
>software package GROMACS back into AMBER.
>I was just wondering without xleap, there is a way I can modify or append
>the amber ff in AMBER.
>I appreciate the help on specific steps I need to follow.
>
>Thanks,
>
>Yao Yao
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Received on Tue Sep 20 2011 - 06:00:02 PDT
