[AMBER] Running Simulations in a Vacuum

From: Juliette Newell <juliette.newell.postgrad.manchester.ac.uk>
Date: Fri, 12 Nov 2021 12:33:51 +0000

Dear Sir/Madam,

I am currently using the amber MD software to run simulations looking at peptide self-assembly.

I am trying to run a simulation in a vacuum, however when I get to the equilibration step I get the error:

'Error: ifbox=2 in prmtop but angles are not correct'

My tleap script is:

source leaprc.gaff2

source leaprc.protein.ff14SB

source keaprc.water.tip3p

CDPA = loadmol2 CDPA.mol2

loadamberparams CDPA2.frcmod

saveoff CDPA2.lib

loadoff CDPA2.lib

solvateoct CDPA CDPA 25

check CDPA

saveamberparm CDPA CDPA2.top CDPA2.crd

Are you able to suggest why I may be getting the error?

Best wishes,

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Received on Fri Nov 12 2021 - 05:00:02 PST
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