Dear AMBER Community,
I am trying to parameterize my system using AMBER force fields, and then do
molecular dynamics with the GROMACS software. I want to use the Lipid17
force field, which is not build into GROMACS. Does anyone know of a way to
do this?
I have found 3 programs people have written to do this, but in short, none
of them work because the codes are too old (ca. 2003).
1)
https://code.google.com/archive/p/amber2gmx/downloads
This would work, but it is written to use a command line parser package
that is too old and I can’t find (com.tsd.apps).
2) The amber2gmxrtp script build into GROMACS
This doesn’t work because it was written to take .in and .prep files (made
for the antiquated AMBER Prep program). Those file types have been
replaced with .lib (made for Leap)
3)The amberconv.tgz package from the GROMACS website (
http://www.gromacs.org/Downloads/User_contributions/Other_software)
This was missing an include file when I tried to compile it.
The reason for using AMBER force fields: My system has lipids, protein,
and a small molecule - all of which can be well described with AMBER force
fields. Since AMBER force fields are QM-based, it would be really easy to
parameterize the small molecule using Antechamber and low-level QM.
GROMACS force fields are empirically derived, so it will be much more
challenging to parameterize the small molecule in a way that’s consistent
with the rest of the force field for lipids and protein. I plan on
simulating more small molecules in the future.
The reason for using GROMACS software: I have nothing against the AMBER MD
package, it’s just a matter of cost and accessibility. I would use AMBER
if I was able to, but GROMACS is free, fast, and also not too difficult to
learn.
Thanks in advance for any advice you’re able to provide!!
Crystal
--
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque
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Received on Wed Jan 03 2018 - 09:00:01 PST
