[AMBER] Some notes

From: erik rp zuiderweg <zuiderwe.umich.edu>
Date: Sat, 14 Jan 2017 20:12:01 +0100

(1) False alarm:
I mentioned that Amber16 (cpptraj) cannot read my old Amber11 trajectories.
I found that some of my old trajectories were corrupted; Amber11 ptraj could not read them either.
No problem in Amber16 reading older bona fide trajectories

(2) leap issue for the manual:
I still have not found in the amber16 manual that with ff14SB one has to explicitly add the water model forcefield
as shown below.
Please update the manual with this script.

source leaprc.protein.ff14SB
source leaprc.water.tip3p
x = loadpdb ./MYPROT.pdb
check x
charge x
set default PBradii mbondi2
solvateBox x TIP3PBOX 7.0
saveamberparm x MYPROT.top MYPROT.crd


Erik Zuiderweg
University of Michigan

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Received on Sat Jan 14 2017 - 11:30:02 PST
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