Re: [AMBER] Changing ligand coordinates

From: Daniel Roe <>
Date: Tue, 26 Feb 2019 10:08:19 -0500


You could use cpptraj to do this. In fact there is a test case in the
cpptraj test directory (Test_CombineCrd) where almost this exact thing
is done. Here I am fitting a modified tyrosine fragment on top of an
existing tyrosine-containing molecule (Tyr.mol2), removing the
overlapping atoms, combining the two, and writing out a mol2 file
which you can then e.g. read into LEaP.

# Load the reference to fit on
parm Tyr.mol2
reference Tyr.mol2 parm Tyr.mol2
# Load the fragment, fit it on top of the existing tyrosine atoms
parm PRY-gauss-fragment.mol2 [pryparm]
loadcrd PRY-gauss-fragment.mol2 parm [pryparm] PRY
# Strip away some overlapping atoms from fragment
crdaction PRY strip .1-4
# RMS fit the fragment (first mask) to the reference (second mask)
crdaction PRY rms reference .O1,C5,C6,C4,H6,H5,C7,C3,H7,H4,C2
# Load the reference for combining
loadcrd Tyr.mol2 parm Tyr.mol2 TYR
# Strip away some overlapping atoms from the reference
crdaction TYR strip !.C,O,CA,HA,N,H,CB,HB2,HB3
# Combine the reference and the fit fragment
combinecrd TYR PRY parmname Final.PRY crdname Final
# Create bond (note: does NOT create parameters)
change crdset Final addbond .CB .C2
# Write out
crdout Final Final.PRY.mol2

Hope this helps,


On Tue, Feb 26, 2019 at 8:29 AM D. Yousefi <> wrote:
> I have the .top, .crd, and .pdb files for a particular small molecule,
> generated by tleap from Amber's force fields. How can I change the
> coordinates of this molecule? (Actually, I want to superimpose it on a
> particular co-crystallized ligand, which have the same structure)
> _______________________________________________
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Received on Tue Feb 26 2019 - 07:30:02 PST
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