AMBER Archive (2009)

Subject: [AMBER] Changing Force Fields in "Midstream"

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Mon Mar 09 2009 - 19:12:27 CDT

Amber Users,

 

Briefly, is there a convenient way to change force fields in the middle
of a fairly long series of runs for a particular system? Specifically,
I'm using Amber 9 but I also have recently installed Amber Tools. My
system is a 12-mer duplex DNA molecule in explicit TIP3P water with a
truncated octahedral box. I want to carry out MM_PBSA calculations on
the system and have gone through a moderately long (for me) heating,
density stabilization and final equilibration (2 ns) process using the
ff99 force field. I just became aware that I probably should have been
using ff99bsc0 plus the updated ion parameters.

 

Using the existing .rst and .prmtop files, I would like to create a new
(ff99bsc0 + ions_08) .prmtop file that contains the same number of water
molecules and has the identical box size, so I can continue with more
equilibration calculations and then a production run. Thus, I would
greatly appreciate learning of some more direct approach, say using
xleap, perhaps in conjunction with ptraj to accomplish my goal.
Presumably, I could edit the .prmtop file, although that approach seems
like a last resort. Thanks in advance.

 

Bob Hopkins

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber