This is good to know - although does anyone know how one goes about getting a residue name 'assigned' in the PDB? I couldn't find DLPC (or it's constituents) in there - although I have to admit to not looking hard.
That said we still need a solution for what to do when:
1) No PDB definition exists - perhaps reduce what we load in one go so rarely used things are not always loaded? (although this goes against what I think is a nice idea of having a default force field file).
2) There are clashes in residue names - do we have anyone who could volunteer to modify leap to detect / warn about this.
3) There are clashes in atom types - same as 2 + how do we plan to coordinate this?
All the best
Ross
> On Mar 24, 2015, at 10:10 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
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Received on Tue Mar 24 2015 - 12:30:03 PDT
