Docswiki - Recent changes [en]

VMD

Dw34 — Sun, 12 Apr 2026 07:53:40 GMT

← Older revision		Revision as of 07:53, 12 April 2026
(One intermediate revision by the same user not shown)
Line 47:		Line 47:
	and Y=(n+1)*m		and Y=(n+1)*m

	m is the number of atoms plus two.		m is the number of atoms plus two. If the total number of frames is not a multiple of n
			then some frames will be lost at the end. Padding the start and finish of the xyz file with copies of the
			initial and final minimum will make the movie pause at these end points.

	To make the movie pause at the start and finish, just duplicate these end points sufficiently. If there are		To make the movie pause at the start and finish, just duplicate these end points sufficiently. If there are

Building tleap

Dw34 — Tue, 07 Apr 2026 14:30:29 GMT

← Older revision		Revision as of 14:30, 7 April 2026
Line 1:		Line 1:
			To start from the tarball :

			bunzip2 AmberTools20.tar.bz2
			tar -xvf AmberTools20.tar
			cd amber20_src

			export AMBERHOME=`pwd`

			If there are missing packages you may need an install:

			apt-get install csh flex gfortran g++ xorg-dev zlib1g-dev libbz2-dev patch python-tk python-matplotlib


			To set up the environment variables use
	source /home/wales/ambertools2/amber20_src/amber.sh		source /home/wales/ambertools2/amber20_src/amber.sh
			whichcould go in ~/.bashrc

Building tleap

Dw34 — Tue, 07 Apr 2026 14:28:11 GMT

Created page with "source /home/wales/ambertools2/amber20_src/amber.sh in ~/ambertools2/amber20_src/AmberTools/src/leap make make install now tleap and teleap are in ~/ambertools2/amber20_src/bin which tleap ~/ambertools2/amber20_src/bin/tleap now it should be possible to do tleap -f leap.in"

New page

source /home/wales/ambertools2/amber20_src/amber.sh

in ~/ambertools2/amber20_src/AmberTools/src/leap

make
make install

now tleap and teleap are in

~/ambertools2/amber20_src/bin

which tleap

~/ambertools2/amber20_src/bin/tleap

now it should be possible to do

tleap -f leap.in

AMBER

Dw34 — Tue, 07 Apr 2026 14:22:58 GMT

← Older revision		Revision as of 14:22, 7 April 2026
Line 12:		Line 12:
	* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]		* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
	* [[Generating parameters using RESP charges from GAMESS-US]]		* [[Generating parameters using RESP charges from GAMESS-US]]
			* [[Building tleap]]
	* [[Simple scripts for LEaP to create topology and coordinate files]]		* [[Simple scripts for LEaP to create topology and coordinate files]]
	* [[Preparing an AMBER topology file for a protein system]] - step by step guide		* [[Preparing an AMBER topology file for a protein system]] - step by step guide