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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Received on Tue Mar 24 2015 - 10:30:03 PDT
