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

Hi,

     Try use ions94.lib to replace ions08.lib.

     The problem is in ions08.lib, the atom type for Magnesium was set
to Mg+
which is wrong, it should be MG. ions94.lib does not have this problem.

     Sincerely,

     Wei

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
> (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
> /usr/local/amber10/dat/leap/parm/frcmod.ionsjc_tip3p
>
> 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,
> but
> 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
> 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
> command.
>
> 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,
> Ross
>
>> -----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
> 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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>
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