Thank you for the email.
> when you say "parameterizing the dimer" do you mean developing force field
> parameters, or making a prmtop?
I mean both. I make an frcmod file that is particular to the dimer and
make a dimer.prmtop and inpcrd from that using leap, all successfully.
> in any case, you should still almost certainly use the 60-mer (or
> whatever)
> using leap, not addles. if you don't give amber the pdb file with all 60
> units it will have no idea where to place them in space.
That is why I was using pack=2 in the addles.in file and concatenating the
input coordinate files (similar to the neb tutorial), but having no
success printing the end .inpcrd file.
> and no, you can't use just the dimer prmtop to simulate everything. the
> prmtop has much more information than just atom info- it tells Amber how
> many atoms, how many residues and so on. these must correspond to the
> entire system. you should try to use the same Leap procedure that you used
> for the dimer, but instead give it the 60-mer pdb file and all of the
> other
> information about force field, if any.
Except the entire system is just 60X repeated dimer units with the same
parameters.
With thanks,
Jenny
> On Tue, Nov 8, 2011 at 11:10 AM, Jenny C Brookes
> <j.brookes.ucl.ac.uk>wrote:
>
>>
>>
>> > no addles won't work, since it replicates the atoms in the same
>> positions.
>>
>> I thought that would work: as long as I just do one copy (with no images
>> on top of the same coordinates) for each dimer position as a trick to
>> make
>> one large inpcrd file (in the test run I was going for 2 parts but the
>> idea ultimately is to go for 60) and one large prmtop file.
>>
>> > I'm not sure why you aren't loading the original coordinates into
>> Leap-
>> > the
>> > geometry is getting lost when you only load the dimer. Maybe you can
>> keep
>> > trying to tell us what information you have and what you want to do-
>> why
>> > split into 60 mol2 files?
>>
>> I have one large .pdb file with 60 x dimer units. The dimers are a
>> repeated unit that form 2 concentric rings. 30 in each ring. Each dimer
>> is
>> 224 atoms. I first ran a simulation parameterizing the dimer only and
>> now
>> I would like to simulate the 2 concentric rings.
>>
>> Since the dimer is the repeating unit then I only really need one
>> .prmtop
>> file to describe all the interactions but I need all the 60 X .inpcrd's
>> so
>> I can describe the particular geometry. I am running namd for the MD
>> simulation and there does not appear to be a way to use the same prmtop
>> file for several coordinates (?). So I am trying to make one large
>> prmtop
>> file and one large inpcrd file and I thought addles might be a way.
>>
>> I have tried using tleap to solve this problem:
>>
>> So I create a .lib file for the dimer:
>>
>> tleap -f leaprc.ff99SB
>>
>> source leaprc.gaff
>>
>> LIG=loadmol2 dimer.mol2
>>
>> check LIG
>>
>> loadamberparams dimer.frcmod (as parameterized from previous simulation)
>>
>> saveoff LIG dimer.lib
>>
>> saveamberparm LIG dimer.prmtop dimer.inpcrd
>>
>>
>> Then to parameterize for all 60 dimers:
>>
>> tleap -f leap.ff99SB
>>
>> source leaprc.gaff
>>
>> loadamberparams dimer.frcmod
>>
>> loadoff dimer.lib
>>
>> ring=loadpdb ring.pdb
>>
>> saveamberparm ring ring.prmtop ring.inpcrd
>>
>> quit
>>
>>
>> Although the .pdb file is never read correctly in the loadpdb step and
>> the
>> parameter files are never created. I have checked the .pdb is in AMBER
>> compatable notation and each dimer (LIG)is separated by TER, but then
>> there appears to be trouble with duplicate atom names. So I became stuck
>> at this point also.
>>
>> Sorry If I haven't explained the problem too clearly. Any more guidance
>> is
>> much appreciated.
>>
>> Best wishes,
>> Jenny
>>
>>
>>
>>
>>
>>
>> >
>> >
>> >
>> > On Mon, Nov 7, 2011 at 3:13 PM, Jennifer Brookes
>> > <j.brookes.ucl.ac.uk>wrote:
>> >
>> >> Yes, that is what I would like. I have a specific geometry for the
>> >> 60dimers
>> >> that I can split into 60 dimer .mol2 files and I was then hoping I
>> could
>> >> use
>> >> addles to stitch back together one .prmtop and one .inpcrd. The
>> dimers
>> >> have
>> >> long range order like a crystal lattice. If addles is not suitable
>> and
>> >> if
>> >> anyone knows of an alternative, that would be much appreciated.
>> >>
>> >> With thanks,
>> >> Jenny
>> >>
>> >>
>> >> -----Original Message-----
>> >> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
>> >> Sent: Monday, November 07, 2011 1:38 PM
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] addles "old coordinate file not specified"
>> >>
>> >> I don't think addles will do this. It sounds like you want a tool
>> that
>> >> can
>> >> build higher-order structures, but it still isn't clear if you are
>> >> looking
>> >> for a specific geometry for the 60 molecules, such as a crystal
>> lattice.
>> >>
>> >>
>> >>
>> >> On Mon, Nov 7, 2011 at 1:01 PM, Jennifer Brookes <j.brookes.ucl.ac.uk
>> >> >wrote:
>> >>
>> >> > I am using pack 2 as I have 2 coordinates in dimer.inpcrd (to
>> create
>> >> > inpcrd for the 2 dimers) and I would like in principle to be able
>> to
>> >> > use this tool for 60 coordinates. I don't actually want to use neb
>> I
>> >> > was just following and modifying the instructions from the tutorial
>> as
>> >> > a way to create .prmtop and .incrd files for many molecules with
>> the
>> >> > same .prmtop specification (as in my first email). So I do not want
>> >> > many images of the dimer for a conformation search I just want to
>> copy
>> >> > one so all have different coordinates. There is probably a better
>> way,
>> >> but
>> >> I do not know what it is.
>> >> >
>> >> > To run addles I have been using amber10.
>> >> >
>> >> > With thanks,
>> >> > Jenny
>> >> >
>> >> > -----Original Message-----
>> >> > From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
>> >> > Sent: Monday, November 07, 2011 12:29 PM
>> >> > To: AMBER Mailing List
>> >> > Subject: Re: [AMBER] addles "old coordinate file not specified"
>> >> >
>> >> > not sure if this is the issue, but could it be the "pack 2" part?
>> >> > it's hard to help without knowing why you want to use addles. are
>> you
>> >> > planning NEB? if yes, which Amber version? for Amebr 11 NEB does
>> not
>> >> > use LES any more.
>> >> >
>> >> >
>> >> >
>> >> > On Mon, Nov 7, 2011 at 12:25 PM, Jennifer Brookes
>> >> > <j.brookes.ucl.ac.uk>wrote:
>> >> >
>> >> > > Dear Amber users,
>> >> > >
>> >> > >
>> >> > >
>> >> > > I have .prmtop and .inpcrd files for a dimer unit which is one
>> >> > > lattice unit that makes up an ordered assembly. I would like to
>> make
>> >> > > input files for the whole assembly (x60 of the dimer unit). So I
>> >> > > have one prmtop file that describes all interactions
>> (dimer.prmtop)
>> >> > > and several coordinate files. To do this, just to test the
>> >> > > principle, I have first tried using addles to generate the input
>> >> > > files for a pair of dimer units. So I try a script
>> >> > > addles.in:
>> >> > >
>> >> > >
>> >> > >
>> >> > > file rprm name=(dimer.prmtop) read
>> >> > >
>> >> > > file ucrcd name=(dimer.inpcrd) pack 2 read
>> >> > >
>> >> > > file wprm name (neb.prmtop) wovr
>> >> > >
>> >> > > file uwcrd name(neb.inpcrd) wovr
>> >> > >
>> >> > > action
>> >> > >
>> >> > > omas
>> >> > >
>> >> > > space numc=2 #prt 1 224 done
>> >> > >
>> >> > > *EOD
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > > addles < addles.in > addles.out
>> >> > >
>> >> > >
>> >> > >
>> >> > > But the inpcrd file is not read or re-written and I get the
>> >> > > following error in addles.out:
>> >> > >
>> >> > > 'Warning-old coordinate file not specified'
>> >> > >
>> >> > > 'New Coordinate file will not be created'
>> >> > >
>> >> > >
>> >> > >
>> >> > > The .prmtop file is written but not the .inpcrd file. If I create
>> >> > > the neb.inpcrd by hand and view neb.prmtop and neb.inpcrd in VMD
>> the
>> >> > > atom assignments are all wrong for the 2 dimer units.
>> >> > >
>> >> > >
>> >> > >
>> >> > > If I follow the instructions in the 'nudged elastic band'
>> tutorial:
>> >> > >
>> >> > >
>> >> > >
>> >> > > http://ambermd.org/tutorials/advanced/tutorial5_amber9/section3.htm
>> >> > >
>> >> > >
>> >> > >
>> >> > > I also get similar issues (the .prmtop file is generated ok, but
>> not
>> >> > > the .inpcrd). Please does anybody see what the problem may be?
>> >> > >
>> >> > >
>> >> > >
>> >> > > With thanks,
>> >> > >
>> >> > > Jenny
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > > _______________________________________________
>> >> > > AMBER mailing list
>> >> > > AMBER.ambermd.org
>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> > >
>> >> > _______________________________________________
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>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> >
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Received on Tue Nov 08 2011 - 10:30:04 PST
