Thank you, that's an interesting way of doing that.
On Tue, Feb 26, 2019 at 6:38 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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
> .OH,CZ,CE1,CE2,HE1,HE2,CD1,CD2,HD1,HD2,CG
> # 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,
>
> -Dan
>
> On Tue, Feb 26, 2019 at 8:29 AM D. Yousefi <da.yousefi.gmail.com> 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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> > AMBER.ambermd.org
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>
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Received on Wed Feb 27 2019 - 04:00:02 PST
