Re: [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps?

From: Ying-Chieh Sun <>
Date: Wed, 17 Sep 2014 09:41:42 +0800

After a quick look, maybe, it is because :1 and :2 were both scmasked, which
is not typical setting in 3-step mutational protocol. HTH.

-----Original Message-----
From: Lawrenz, Morgan []
Sent: Wednesday, September 17, 2014 9:01 AM
To: AMBER Mailing List
Subject: [AMBER] For Amber14 TI, how to perform only the discharge/recharge

Hi all,
I am trying to use Amber14 to perform TI and compute relative free energies
between two molecules.
I'm working with a test system, two molecules in vacuum, and have reviewed
the manual for the new single topology approach, along with recent tutorials
I've successfully used before with the dual topology approach:

I've planned 3 steps, one to discharge molecule1, one to scale the vdw
parameters from molecule 1 to molecule 2, and a third step to recharge
I have step 2 running successfully (after turning off SHAKE) but have been
unable to get step 1 going using the new flags. I am not sure if I
understand the manual correctly.
For step 2, I made a topology with leap using a pdb of the two different
molecules. For step 1, I thought that I needed to build a topology with a
pdb file of two molecule1 structures (which are exactly the same), numbered
residue 1 and 2 in the pdb file. The molecules have the same residue name.
Then I specified the v0 and v1 atoms with timask1=":1" , timask2=":2" and
then just use a charge mask for residue 2 (where I want partial charges
I kept getting "Bus errors" and then turned off SHAKE and still am getting a
segmentation fault when performing minimization.
Segmentation fault /common/compchem/src/amber14/bin/pmemd -O -i -o min-fep.out -p ../ -c ../phenols.crd -x
min-fep.netcdf -r min-fep.rst

Here is my input file for minimization, please let me know if I am missing
minimization fep
  imin = 1, ntmin=2, ntx = 1,
  ntpr = 100,
  ntf = 1, ntc = 1,
  ntb = 1, cut = 9.0,

Thanks a lot for the help! And let me know if any more info is helpful here.
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Received on Tue Sep 16 2014 - 19:00:02 PDT
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