Hi all,
I want to perform a gas-phase protein simulation (to compare with gas phase structural biology experiments) using the AMOEBA ff.
Specifically, I'm trying to get AMBER topology & coordinates for a nonperiodic AMOEBA gas phase simulation, using tinker_to_amber on a test case of ubiquitin.
The conversion for prmtop and inpcrd files is fine when I specify a box size with a-axis, and some ewald keywords in the keyfile, similar to the info in the /examples folder in the pmemd.amoeba build directory. But running tinker_to_amber without any box info gives a complaint of "No box information in XYZ or .key file" and no output.
The only info about vacuum simulations I've found in the TINKER manual is this:
EWALD-BOUNDARY This keyword invokes the use of "vacuum" boundary conditions during Ewald summation, corresponding to the media surrounding the system having a dielectric value of 1.
The manual does mention capability with both periodic and non-periodic systems, but I'm not sure if there's a way to specify the non-periodicity, beyond just leaving out the periodic info.
Can you give any tips on if/ how I can accomplish this? I'm aiming to run this with pmemd.amoeba but do not think my current input files (that I've used successfully with the fixed charge ff14) will work here, because to run in vacuum in pmemd I use igb=1 with extdiel=1.0 (got this from the mail archives) and I think this is not allowed for use with amoeba.
To run minimization using pmemd:
&cntrl
imin = 1,
maxcyc = 20000,
ntb = 0,
igb = 1,
extdiel = 1.0,
cut = 999
/
To run minimization is sander:
&cntrl
imin = 1,
maxcyc = 20000,
ntb = 0,
igb = 0,
cut = 999
/
I'm using a pretty basic keyfile here for tinker_to_amber - since most run parameters will be in the AMBER inputs, and have tried this with and without the ewald-boundary keyword:
parameters amoebabio09
verbose
# Want non periodic system with dielectric=1
ewald-boundary
Thanks for any help!
Morgan
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Received on Mon Dec 15 2014 - 12:30:02 PST
