AMBER force field


#1

Hello,

I need to perform a MD simulation using GROMACS and I need to use AMBER force field.
I see that 99sb-ildn is the most recent version included in the package. I also found a page
with user-contributed ports of more recent versions of the force field:
http://www.gromacs.org/Downloads/User_contributions/Force_fields

I wondered if I should stick with the ones provided in the GROMACS package or use the ones
provided in that page. There is an instruction there about “testing the results for correctness”.
I am not so experienced to do this therefore is there a standard procedure to do this or I should stick
with the older versions? Should I check for steric clashes or atom overlaps (any suggestion for such
a tool?). In the AMBER manual it is advised to use the more recent versions though (like Amber14SB,
the one that I would like to use).

I downloaded a 14SB port provided in the force fields page but it includes files from the older versions
unchanged. How trustworthy is it?

Thank you in advance.


#2

As you’ve seen, those user contributions are offered on a “I think these might be useful” basis. Validating a force field tends to mean showing that a set of relevant single-point energy calculations work the same way in the original implementation (ie in AMBER software) and the new one. Those might well relate to the set of calculations they did when parameterizing, so someone needs to find out what exists and port it to GROMACS formats, etc. People tend not to want to do that, so such force fields don’t go into official GROMACS distributions, because if they were, then everyone would assume such testing had happened.

You should already know whether 14SB was a complete re-work of all or part of the force field, so probably some unchanged files are to be expected.


#3

Thank you for your reply. I found this for anyone interested : http://bionano.physics.illinois.edu/CUFIX

They distribute a GROMACS port of ff99sb-ildn-phi-bsc0 version with additional fixes (“cufix”) so I will give it a try.
I need the bsc0 parameters.

Edit:
More on the subject: http://ffamber.cnsm.csulb.edu/ffamber.php#usage