AMBER Archive (2009)
Subject: Re: [AMBER] Changing Force Fields in "Midstream"
From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Wed Mar 11 2009 - 16:42:52 CDT
Try use ions94.lib to replace ions08.lib.
The problem is in ions08.lib, the atom type for Magnesium was set
which is wrong, it should be MG. ions94.lib does not have this problem.
On Mar 11, 2009, at 4:36 PM, Hopkins, Robert wrote:
> 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
> 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 http://archive.ambermd.org/200807/0104.html 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,
> I'm not sure where. Any help would be greatly appreciated. Thanks!
> Bob Hopkins
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] 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
> current restart file that you have. The caveat is that the atom
> 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
> to run these through leap again substituting ff99 for ff99bsc0. The
> issue might be if there are any changes in VDW radii (not sure if
> be - there might be for ions but I didn't check) which would lead to
> solvate command not giving the exact same number of waters or ions.
> 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: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of Hopkins, Robert
>> Sent: Monday, March 09, 2009 5:12 PM
>> To: AMBER_at_ambermd.org
>> 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
>> the system and have gone through a moderately long (for me) heating,
>> density stabilization and final equilibration (2 ns) process using
>> 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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