AMBER Archive (2009)

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

From: Hopkins, Robert (
Date: Wed Mar 11 2009 - 16:36:12 CDT

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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