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

From: Hopkins, Robert <>
Date: Tue, 10 Mar 2009 18:29:44 -0500

Dr. Walker,

Thanks very much for your help!

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 Wed Mar 11 2009 - 01:28:59 PDT
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