[AMBER] All working now, except some trajectories

From: erik rp zuiderweg <zuiderwe.umich.edu>
Date: Wed, 11 Jan 2017 16:48:22 +0100

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

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

AMBER mailing list
Received on Wed Jan 11 2017 - 08:00:03 PST
Custom Search