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

From: Kristina Furse <>
Date: Wed, 11 Mar 2009 17:58:06 -0400

Hi Bob-

Sorry this is kind of late--it's probably irrelevant to your new ion problem, but I'll go ahead and post this anyway. I've had to do this kind of thing before, so I came up with a trick so I don't have to rebuild the box.

First, take your existing .rst and prmtop files and make a pdb:

ambpdb -p parmtop < orig.rst > DNA.pdb

Then read this pdb of your entire system into xleap after loading the new force field, and use the setbox command to say there is a box w/out building a new one:

source leaprc.ff99
loadamberparams ~/solDynProject/prep_frcmod/parmbsc0/frcmod.parmbsc0
loadoff ~/solDynProject/prep_frcmod/parmbsc0/DNA_CI.lib
dna = loadpdb DNA.pdb
setBox dna centers
saveamberparm dna new.parmtop junk.dat

Throw away junk.dat b/c it will have the wrong box--just use your orig.rst. Now, here I go through some extra steps to b/c I'm paranoid. In the new.parmtop file, I go to the %FORMAT section and change the "box" flag from 1 (cubic) to 2 (truncated octahedron). It is the third number from the right in the third line (you can find a description of the parmtop file format on the amber website). Then I go down to the %FLAG BOX_DIMENSIONS section and replace it with the same section from my original parmtop. I believe that these things aren't really used anymore, or they are overridden by information at the bottom of the restart file after the initial run, but like I said, I'm paranoid and this method gives me a parmtop with the new force field that is in every other way identical to my original one. Like Ross said, be sure to use ambpdb to double check that the new parmtop is compatible with your orig.rst and builds the same structure.

Good luck!


Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556
From: [] On Behalf Of Hopkins, Robert []
Sent: Wednesday, March 11, 2009 5:36 PM
To: AMBER Mailing List
Subject: RE: [AMBER] Changing Force Fields in "Midstream"
Amber Users,
Based on Ross Walker's suggestion, I attempted to build a new .prmtop
file using a modified leaprc.ff99bsc0 script where ions08.lib replaced
ions94.lib and the command mods = loadAmberParams frcmod.ionsjc_tip3p
was added.  Then, using my original PDB file (IRdna.pdb) in xleap (Amber
Tools 1.2) -- I (essentially) did the following:
IR = loadPdb IRdna.pdb
addions IR Mg+ 0
solvateOct IR TIP3PBOX 8.0
All appeared to go well, except that I got a message: "(type - hence
mass - of one or more atoms could not be found)".  The result was that
the command:
saveAmberParm IR IRnew.prmtop IRnew.inpcrd
came back with a message for each ion like:  "For atom: .R<Mg+
4140>.A<Mg+ 1> could not find type: Mg+" and xleap would not write out
either file.  For grins, I tried changing the order of adding ions vs.
solvating but got the same result.  I also tried loading xleap with
leaprc.ff99bsc0 and then adding the modifying commands
loadoff /usr/local/amber10/dat/leap/lib/ions08.lib
mods = loadAmberParams
But, once again, to no avail.  It is fairly clear that I'm missing
something important here, but I didn't find much of relevance in the
archives except although
that didn't provide me an answer.  I'm concerned that the unit name
(mods) for frcmod.ionsjc_tip3p should be specific or used somewhere, but
I'm not sure where.  Any help would be greatly appreciated.  Thanks!
Bob Hopkins
-----Original Message-----
From: [] On
Behalf Of Ross Walker
Sent: Monday, March 09, 2009 7:21 PM
To: 'AMBER Mailing List'
Subject: RE: [AMBER] Changing Force Fields in "Midstream"
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
total number of atoms needs to be identical. Assuming you have the
scripts you used to build the prmtop and inpcrd file you should just be
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
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
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
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
match what they should be before 'restarting' the MD with the new
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
> of a fairly long series of runs for a particular system?
> 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
> using ff99bsc0 plus the updated ion parameters.
> Using the existing .rst and .prmtop files, I would like to create a
> (ff99bsc0 + ions_08) .prmtop file that contains the same number of
> 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
> like a last resort.  Thanks in advance.
> Bob Hopkins
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Received on Fri Mar 13 2009 - 01:15:16 PDT
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