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

From: David Wright <david.wright.gtn.ai>
Date: Sat, 4 Jan 2020 13:10:03 +0000


I am writing an automated pipeline for some simulations and would like to
be able to create caps around a group of selected atoms. I have tested this
using the tleap input script below:

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
Tarball of inputs (including script) here:

The input protein contains 164 residues and I am aiming to create the cap
around the ligand (residue 165). The output is a cap around the final
protein residue (164).

- Using the command `desc capCentre` when running the commands manually I
see the correct atoms listed.
- Using `solvatecap complex TIP3PBOX complex.165 20 1.0` creates the
correct output.

Is this just not something that can be done, am I making a mistake or is
there a bug? The reason I want to do this I have tried above is that it is
easier in my workflow to create the selections incrementally (for more
complex situations than this test).

Dave Wright
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Received on Sat Jan 04 2020 - 05:30:02 PST
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