Alright, I remade the parameter files and everything is good both in AMBER
and OpenMM. I'm not sure what would have been the problem before, but
there is a chance I made those right after AMBER 12 came out, and I might
have used AmberTools 11 with the FF12SB forcefield, could that have been a
problem?
Anyway, everything seems good now, thanks for the reply!
~Aron
On Tue, Oct 16, 2012 at 2:40 PM, Aron Broom <broomsday.gmail.com> wrote:
> Yeah, I guess I'll have to check more thoroughly the process I used to
> make those files.
>
> I made a (GLY-ALA)x5 decapapetide, and the bonds were properly
> restrained. It was only within the context of my full length protein that
> this wasn't happening.
>
> I'll check with AMBER as you suggest. I suspected it would probably take
> more thorough work, but hoped maybe it was a known issue.
>
> I'll report back once I've nailed down the issue.
>
> ~Aron
>
>
> On Tue, Oct 16, 2012 at 1:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Tue, Oct 16, 2012 at 12:59 PM, Aron Broom <broomsday.gmail.com> wrote:
>>
>> > I recently used tleap within AMBER tools version 12, to generate some
>> > protein parameter files, using AMBER_FF12SB.
>> >
>> > The command structure was:
>> >
>> > > set default PBradii mbondi2
>> > > model = loadpdb protein.pdb
>> > > saveamberparm model protein.prmtop protein.inpcrd
>> >
>> > Everything seemed to be working fine, but in trying to troubleshoot a
>> > temperature problem I was having with OpenMM, I realized that some of
>> the
>> > glycine (CA-HA2 and CA-HA3) bonds were not being properly constrained.
>> It
>> > looking at the .prmtop file, it looks as though those bonds were not
>> added
>> > to the BONDS_INC_HYDROGEN list.
>> >
>>
>> This would shock me. If you create a sequence ACE-GLY-NME in leap and
>> save
>> the prmtop, you can clearly see the CA-HA2 and CA-HA3 bonds in the
>> BONDS_INC_HYDROGEN section. In this case, I would be less likely to
>> suspect tleap than OpenMM (tleap is significantly older and more
>> thoroughly
>> tested).
>>
>> I haven't done any of the bugfixes for ambertools 12, but I don't see
>> > anything about that listed. Is this something that anyone else has
>> seen?
>> > I haven't done a rigorous test to ensure it is reproducible, thought I
>> > would see if anyone else has noted this kind of problem before. As an
>> FYI,
>> > the input pdb files I was using don't have hydrogens at all, so there
>> > shouldn't have been any problem with LeAP not recognizing the atom name.
>> >
>>
>> What happens if you run it through sander or pmemd? Sander reports the
>> DOF
>> in your system, properly adjusted for SHAKE constraints. Therefore, you
>> should be able to use sander with "noshakemask" targeting the problematic
>> residues and see if the DOF changes between the two simulations. If the
>> DOF changes, then sander knows to SHAKE them, further suggesting OpenMM as
>> the culprit.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Oct 16 2012 - 16:30:05 PDT
