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

From: David Wright <david.wright.gtn.ai>
Date: Mon, 6 Jan 2020 11:37:59 +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
AMBER mailing list
Received on Mon Jan 06 2020 - 04:00:02 PST
Custom Search