AMBER Archive (2009)

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

From: Ross Walker (
Date: Mon Mar 09 2009 - 19:21:15 CDT

Hi Robert,

In theory you can build yourself a new prmtop file and use this with the
current restart file that you have. The caveat is that the atom ordering and
total number of atoms needs to be identical. Assuming you have the original
scripts you used to build the prmtop and inpcrd file you should just be able
to run these through leap again substituting ff99 for ff99bsc0. The only
issue might be if there are any changes in VDW radii (not sure if there will
be - there might be for ions but I didn't check) which would lead to the
solvate command not giving the exact same number of waters or ions. This you
will have to try to deal with by tweaking the buffer value to the box

Before running with the new prmtop I would pass this prmtop + the current
restart file to ambpdb and or ptraj to generate a pdb file from this
combination and then check that it all looks reasonable and the atoms all
match what they should be before 'restarting' the MD with the new prmtop.

Good luck,

> -----Original Message-----
> From: [] On
> Behalf Of Hopkins, Robert
> Sent: Monday, March 09, 2009 5:12 PM
> To:
> Subject: [AMBER] Changing Force Fields in "Midstream"
> 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
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