source leaprc.ff10 loadamberparams frcmod.ionsjc_tip3p set default PBradii mbondi2 1vom = loadpdb 1vom-clean.pdb addions 1vom Na+ saveamberparm 1vom prmtop inpcrd
########### resolve a problem
export AMBERHOME=`pwd` root@shenzy-pc:/home/shenzy/lib/amber14# ./update_amber –apply leap.patch export AMBERHOME=`pwd` ./update_amber –apply http://ambermd.org/bugfixes/AmberTools/13.0/cygwin_fix
root@shenzy-pc:/home/shenzy/lib/amber14# cat leap.patch *******>leap.patch
Author: Jason Swails
Date: 30 April, 2014
Programs: tleap, xleap
Description: Solves potential inpcrd file truncation […]
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