I now have Amber16 and Ambertools 16 running on a Mac, running 10.11.6 (El Capitan),
using Xtools 8.2.1, and gnu gfortran-6.1.2 (renamed to gfortran), and the clang cc and g++ compilers with Python 2.7.,
following the instructions in the Amber16 manual using
./install -macAccelarate clang
However, the Amber16 manual needs an update on leap; coming from Amber11, I had no idea why I could not embed my protein in a TIP3PBOX.
Turns out that the water models are now in an other forcefield (since ???). Please update the manual!
This worked for me:
source leaprc.protein.ff14SB
source leaprc.water.tip3p
x = loadpdb ./BETA_TAU1a_WAT_MIN_HEAT_PROD_COOL.pdb
check x
charge x
set default PBradii mbondi2
solvateBox x TIP3PBOX 7.0
saveamberparm x BETA_TAU1a_WAT.top BETA_TAU1a_WAT.crd
quit
I am still puzzled why cpptraj does not recognize the format of old trajectory files generated with amber11.
Please help??
Decided to rerun some for now.
Erik Zuiderweg
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Received on Wed Jan 11 2017 - 08:00:03 PST
