Hi,
Thanks for the reply.
The simplified version works fine (including using that method in the
script I provided) - the reason I want to use groups is it would allow me
to programmatically create a script where the selection may be more complex
(for example containing a combination of atoms and residues).
As a side note - the cap is applied to the final residue of the protein no
matter what set of atoms is selected to form the group.
Cheers
Dave
On Mon, Jan 6, 2020 at 2:38 PM David Case <david.case.rutgers.edu> wrote:
> On Mon, Jan 06, 2020, David Wright wrote:
> >
> >```
> >source leaprc.protein.ff14SB
> >source leaprc.water.tip3p
> >source leaprc.gaff
> >loadAmberParams lig.frcmod
> >mol0 = loadPdb rec.pdb
> >mol1 = loadMol2 lig.mol2
> >complex = combine { mol0 mol1 }
> >select complex.165
> >groupSelectedAtoms complex capCentre
> >deSelect complex
> >solvatecap complex TIP3PBOX complex.capCentre 20 1.0
> >saveAmberParm complex complex.prmtop complex.inpcrd
> >savePDB complex complex.pdb
> >quit
>
> I don't think what you have above will work: are the coordinates in the
> lig.mol2 file in the correct position relative to the rec.pdb file?
>
> My preference is always to first create a pdb file with the entire
> system in it ("complex.pdb"). You can examine this file visually, and
> this is what a docking program would typically create.
>
> Whether or not you do the above, try a simpler version of your script:
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> source leaprc.gaff
> loadAmberParams lig.frcmod
> complex = loadPDB complex.pdb
> desc complex.165 <== just to see if this is indeed your ligand
> solvatecap complex TIP3PBOX complex.165 20 1.0
> saveAmberParm complex complex.prmtop complex.incprd
> savePDB complex complex.cap.pdb
>
> There is no need to groupSelectedAtoms, etc: just giving a RESIDUE
> (complex.165) in the solvateCap command should do what you want.
>
> I haven't tried the above, but it's worth you time to see if it helps.
>
> ....dac
>
>
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Received on Tue Jan 07 2020 - 04:00:02 PST
