Thanks. I was able to run minimization and MD with this input for a discharge step:
minimization fep
&cntrl
imin = 1, ntmin=2, ntx = 1,
maxcyc=500,
ntpr = 100,
ntf = 1, ntc = 1,
ntb = 1, cut = 9.0,
icfe=1,
clambda=0.0,
timask1=":1",
timask2=":2",
logdvdl=1,
crgmask=":2"
/
-----Original Message-----
From: Ying-Chieh Sun [mailto:sun.ntnu.edu.tw]
Sent: Tuesday, September 16, 2014 6:42 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps?
Hi,
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.
Ying-chieh
-----Original Message-----
From: Lawrenz, Morgan [mailto:mlawrenz.amgen.com]
Sent: Wednesday, September 17, 2014 9:01 AM
To: AMBER Mailing List
Subject: [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps?
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:
http://ambermd.org/tutorials/advanced/tutorial9/setup.html
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 molecule2.
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 gone).
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
min-fep.in -o min-fep.out -p ../phenols.top -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 something!
minimization fep
&cntrl
imin = 1, ntmin=2, ntx = 1,
maxcyc=500,
ntpr = 100,
ntf = 1, ntc = 1,
ntb = 1, cut = 9.0,
icfe=1,
clambda=0.1,
klambda=1,
tishake=1,
idecomp=0,
timask1=":1",
timask2=":2",
ifsc=1,
scalpha=0.5,
scmask1=":1",
scmask2=":2",
logdvdl=1,
crgmask=":2"
/
Thanks a lot for the help! And let me know if any more info is helpful here.
Morgan
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Received on Fri Sep 19 2014 - 11:30:02 PDT
