> 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
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
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>> >
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Received on Tue Nov 08 2011 - 08:30:02 PST
