I tend to agree, and as the pdb is working on this we should coordinate
with them on changes.
On Mar 24, 2015 11:08 AM, "Pawel Janowski" <pawelrc.gmail.com> wrote:
> Hi,
>
> I think we should respect the residue naming assigned by the PDB. That's
> the best way to avoid these types of uncertainty in the future. So if you
> look for LA in http://www.ebi.ac.uk/pdbe-srv/pdbechem/ it turns out it is
> the residue name for La3+. I would keep LA for La3+ and find a different
> name for the other component (or check if one already exists in the PDB
> dictionary; you can search by chemical formula).
>
> Pawel
>
> On Tue, Mar 24, 2015 at 12:51 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi All,
> >
> > Please see the thread below regarding name clashes in leap with residue
> > names. We do indeed need to come up with a more permanent solution for
> this
> > and I am open to suggestions. Perhaps an initial thing to do would be to
> > have leap detect such clashes (and atom types clashes as well) when
> loading
> > leaprc files - this would be a start for us to identify where the clashes
> > are. I am already concerned that we might be getting silent atom name
> > clashes that are leading to people running with different parameters than
> > they think they are.
> >
> > Suggestions?
> >
> > Dan, as an interim fix - given I doubt anyone is actually running
> > simulations with La3+ - that we change the residue name here to avoid
> > issues going forward with AmberTools 15. I suggest LA3 - or La3 or
> > something else that is not currently used.
> >
> > All the best
> > Ross
> >
> > > On Mar 24, 2015, at 9:44 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > >
> > > OK, I believe I've found the issue, and Ben you'll be happy to know
> > > it's not charmmlipid2amber.py. Turns out that "LA" is a residue name
> > > already present in atomic_ions.lib for La3+ (how annoying is that?).
> > > So Kiu, because the order in which you loaded libraries was:
> > >
> > > source leaprc.lipid14
> > > source leaprc.ff12SB
> > >
> > > The LA residue in lipid14 was being silently overwritten by the
> > > loadoff in leaprc.ff12SB. Switching the ordering to:
> > >
> > > source leaprc.ff14SB
> > > loadamberparams frcmod.ionsjc_tip3p
> > > source leaprc.lipid14
> > >
> > > seems to fix the issue.
> > >
> > > .Ross - this should probably be brought up to the dev list (or a
> > > subset thereof) to come up with a better, more permanent solution,
> > > whether it's making leap not overwrite things by default (which could
> > > get ugly), changing names, ensuring load orders are correct etc.
> > >
> > > -Dan
> > >
> > > On Mon, Mar 16, 2015 at 11:18 AM, Benjamin D Madej <bmadej.ucsd.edu>
> > wrote:
> > >> Hi Dan,
> > >>
> > >> Thanks for taking a look! Yes, once I get back next week I can take a
> > look at it. I also plan on writing up some documentation on the
> charmmlipid
> > script so that it is clearer how it works. It is essentially a simple
> > python script for substituting strings and reordering lines in the PDB.
> > >>
> > >> Best,
> > >> Ben
> > >> ________________________________________
> > >> From: Daniel Roe [daniel.r.roe.gmail.com]
> > >> Sent: Monday, March 16, 2015 9:52 AM
> > >> To: Ross Walker
> > >> Cc: Kiumars Shahrokh; Benjamin D Madej
> > >> Subject: Re: DLPC
> > >>
> > >> Excellent, congrats Ben!
> > >>
> > >> I'll pop it into bugzilla in the meantime. If I get ambitious/brave
> > >> maybe I'll wade into the land of python to try and figure it out...
> > >>
> > >> -Dan
> > >>
> > >> On Mon, Mar 16, 2015 at 10:44 AM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> > >>> Ben just finished his PhD and is taking some well deserved vacation.
> > >>>
> > >>> He'll take a look at it once he gets back to work in a week or two.
> > >>>
> > >>> In the meantime yes please add it to bugzilla so it gets tracked.
> > >>>
> > >>> Thanks,
> > >>>
> > >>> All the best
> > >>> Ross
> > >>>
> > >>>> On Mar 16, 2015, at 9:41 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >>>>
> > >>>> Hi All,
> > >>>>
> > >>>> I've had a quick look at this and what I think is happening is that
> > >>>> the PDB that is generated (DLPC-50.pdb) is not valid; in particular,
> > >>>> the atom naming in the tails is messed up. For example, in residue 1
> > >>>> (LA/PC/LA) atom "H2R" appears twice - I think one of them should be
> > >>>> "H2S" maybe? I think "charmmlipid2amber.py" may need some fixing
> > >>>> before the release. Should I create a bugzilla for this? I would
> take
> > >>>> a crack at it but I figured the lipid experts may want dibs on this
> > >>>> one...
> > >>>>
> > >>>> -Dan
> > >>>>
> > >>>> On Fri, Mar 13, 2015 at 1:16 PM, Kiumars Shahrokh <
> Kiu.pharm.utah.edu>
> > wrote:
> > >>>>> Hi Ben and Ross,
> > >>>>>
> > >>>>> I am trying to build a DLPC bilayer following your on-line tutorial
> > for DOPC
> > >>>>> and am having trouble generating the AMBER input files. I can build
> > the
> > >>>>> AMBER inputs (topo/crd) just fine with DOPC following the tutorial.
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> With DLPC I can build the starting “step5_assembly-dlpc50.pdb” with
> > the
> > >>>>> CHARMM GUI, and from that generate a DLPC-50.pdb with
> > charmmlipid2amber.py
> > >>>>>
> > >>>>> From DLPC-50.pdb I can calculate the box size (See attached files)
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> Then running it into tleap (-sf buildit) I get a lot of:
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H10R 27> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H10S 28> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<C111 29> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H11R 30> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H11S 31> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<C112 32> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H12R 33> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H12S 34> does not have a type.
> > >>>>>
> > >>>>> FATAL: Atom .R<LA 300>.A<H12T 35> does not have a type.
> > >>>>>
> > >>>>> Failed to generate parameters
> > >>>>>
> > >>>>> Parameter file was not saved.
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> Not sure what I’m doing wrong or if this is a bug. Please let me
> > know.
> > >>>>>
> > >>>>> Thanks,
> > >>>>>
> > >>>>> Kiu
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> --
> > >>>> -------------------------
> > >>>> Daniel R. Roe, PhD
> > >>>> Department of Medicinal Chemistry
> > >>>> University of Utah
> > >>>> 30 South 2000 East, Room 307
> > >>>> Salt Lake City, UT 84112-5820
> > >>>> http://home.chpc.utah.edu/~cheatham/
> > >>>> (801) 587-9652
> > >>>> (801) 585-6208 (Fax)
> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe, PhD
> > >> Department of Medicinal Chemistry
> > >> University of Utah
> > >> 30 South 2000 East, Room 307
> > >> Salt Lake City, UT 84112-5820
> > >> http://home.chpc.utah.edu/~cheatham/
> > >> (801) 587-9652
> > >> (801) 585-6208 (Fax)
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 307
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
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Received on Tue Mar 24 2015 - 10:30:04 PDT
