Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap

From: David Case <>
Date: Mon, 6 Jan 2020 14:34:20 +0000

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

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.


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Received on Mon Jan 06 2020 - 07:00:03 PST
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