Re: [AMBER] Problem with heating lipid bilayer in amber 12

From: Ross Walker <>
Date: Thu, 19 Mar 2015 14:49:30 -0700

It should work with AMBER 12.

But I don't think you can have comments in the group part of the mdin file:

&wt type='END' / ! End of varying conditions
Hold lipid fixed
10.0 ! Force constant (kcal/(mol Angstroms^2))
RES 1 222 ! Choose residues
END ! End GROUP input

> On Mar 19, 2015, at 2:31 PM, Chris Gaughan <> wrote:
> Hello
> I am following the 'An Amber Lipid Force Field Tutorial: Lipid14 Edition' tutorial. I have performed the first minimization and am now at the first heating step.
> I built AmberTools 14 on my iMac, prepared the lipid bi-layer using the CHARMM-GUI, then made the amber .prmtop and .inpcrd with xleap.
> I transferred the prmtop and inpcrd to however, this cluster only has the Amber 12 versionThe minimization went least it ran without error
> I ran the first heating MD to heat the lipid bilayer using pmemd.MPI. Will such a simulation even work in this version of amber (amber 12)?
> So far I'm getting an error I've not yet seen: rfree: Error decoding variable 4 2 from:RES 1 222 !
> I have attached the .out file for more complete information.
> Thanks for any adviceChris <02_heat.out>_______________________________________________
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Received on Thu Mar 19 2015 - 15:00:06 PDT
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