Hello,
I am trying to obtain the entropy from the output of several MD simulations I performed recently in AMBER on ACE- and NME-capped amino acids; I’m having some difficulty in carrying out the calculation using quasi-harmonic analysis at the moment.
First, I believe I need to obtain an average structure, stripped of solvent, and for that I used the the following input:
parm ~/entropy-md/alanine/setup/ala-solv.prmtop #(topology file of the alanine dipeptide in solution)
trajin ~/entropy-md/alanine/production/ala-solv-prod.mdcrd
autoimage
strip :WAT
average ala-avg.mdcrd crd nobox
This completes successfully, however the next step, the actual QH calculation fails to complete. I used the following script:
parm ~/entropy-md/alanine/setup/ala-vac.prmtop #(topology file of the alanine dipeptide alone)
trajin ala-avg.mdcrd
createcrd ala-avg.nc
crdaction ala-avg.nc mwcovar name arcov out arcov.dat
runanalysis diagmatrix arcov out qh.out thermo outthermo thermo.dat temp 300
The second script seems to fail after createcrd is invoked, and cpptraj reports that the trajectory file contains no frames: the same thing happens when I load in a trajectory with just the solvent removed, but not averaged.
Any help with this would be greatly appreciated.
As an additional request, I would be grateful for any assistance/pointers to guidance for performing normal mode analysis of my output, to obtain entropy using that method as well.
Kind regards,
Mo
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Received on Thu Sep 21 2017 - 09:00:02 PDT
