Update after fixing all errors:
As it turns out, I had fixed the update 4 and 9 errors before! The
$AMBERHOME/update_amber --show-unapplied-patches does not return any value
for unapplied patches. I don't remember exactly but I assume the error was
gone after I solved the issue I had with my Python version.
I can use the NFE toolkit on both sander and pmemd to do steered MD
simulations, however as I remember, the pmemd could not perform any QMMM
runs (there is a &qmmm in my mdin file). Is this still the case in Amber16?
Best,
Sam
On Thu, Apr 13, 2017 at 12:56 PM, Samaneh Ghassabi Kondalaji <
saghassabikondalaji.mix.wvu.edu> wrote:
> I guess I'll do that! I am already having lots of issues with my current
> SMD run! Amber14 works but the simulation now is giving me this error:
> QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
> QMMM SCC-DFTB: Convergence could not be achieved in this step.
> QMMM SCC-DFTB: The calculation will continue, but energies and
> QMMM SCC-DFTB: forces for this step will not be accurate.
> I think I need to go back and check my QMMM equilibration again before
> running SMD. Unfortunately the Amber tutorial on SMD (
> http://ambermd.org/tutorials/advanced/tutorial10/) does not provide much
> of information regarding the initial distance RST file, I used makeDIST to
> generate distance between N atom on a lysine and O of a water molecule on
> my weird system! (http://archive.ambermd.org/201704/0114.html) but
> makeDIST generated a group restraint of 3 H atoms attached to N on Lysine
> (-NH3+) and the oxygen atom on water.
> #
> # 12 LYS NZ 23 WAT O 1.30 3.50
> &rst
> ixpk= 0, nxpk= 0, iat= -1, 270, r1= 0.80, r2= 1.30, r3= 4.20, r4= 4.70,
>
> rk2=20.0, rk3=1000.0, ir6=1, ialtd=0,
> igr1= 140, 141, 142,
> /
> I run two equilibration simulations: one with the RST between O and H
> atoms as single group (igr1) and the second one between N atom and O. The
> one from the group atoms seemed OK but the N and O equilibration lead to
> strange behaviour and as I visualized it, the bond length between N and H
> was increasing like crazy! So I got my replicates for SMD from the
> equilibration of O atom and H-group restraints. However the path on SMD run
> monitors the proton transfer from N to O and has nothing to do with my atom
> selection for the equilibration!
> Will try to solve this problem first and then move to fixing update
> issues. Thank you so much for all your wonderful help!
> Best,
> Sam
>
>
> On Thu, Apr 13, 2017 at 12:35 PM, Hannes Loeffler <
> Hannes.Loeffler.stfc.ac.uk> wrote:
>
>> I am not sure what your problem there is but my suggestions would be to
>> do a fresh download of the AmberTools and then start the update process
>> with the Python tool. But since AmberTools17 are soon to be released
>> you may want to just wait for that.
>>
>> Cheers,
>> Hannes.
>>
>>
>> On Thu, 13 Apr 2017 12:01:35 -0400
>> Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
>>
>> > Thank you for your fast reply. I remember now, this is update.9! I was
>> > getting an error like this one
>> > (http://archive.ambermd.org/201610/0212.html) when I was updating
>> > before installation and couldn't solve it. Reading through update 4
>> > and 9 description at the time (way before my need for nscu!), I
>> > decided to continue without. I will use Amber14 for this particular
>> > run now but I need to fix the problem for future runs, update and
>> > recompile. I would greatly appreciate if you have any suggestion on
>> > how to fix this update issue. Sincerely yours,
>> > Sam
>> >
>> > On Thu, Apr 13, 2017 at 11:40 AM, Hannes Loeffler <
>> > Hannes.Loeffler.stfc.ac.uk> wrote:
>> >
>> > > On Thu, 13 Apr 2017 11:29:59 -0400
>> > > Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
>> > >
>> > > > Dear Amber Users and Developers
>> > > > I am trying to perform a QMMM SMD simulation to monitor a PT
>> > > > reaction. I equilibrated my system and obtained replicates,
>> > > > However when I subject the replicates to SMD using the fallowing
>> > > > parameters and sander.MPI, it seems like sander is not reading
>> > > > the ncsu section and the variables.
>> > >
>> > > I suppose you have applied the recent updates to AmberTools. The
>> > > code (now called NFE) has been changed to read all inputs through
>> > > namelists. See nfe.pdf on http://ambermd.org/bugfixesat.html .
>> > >
>> > >
>> > > Cheers,
>> > > Hannes.
>> > >
>> > > _______________________________________________
>> > > 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
>>
>
>
>
> --
> *Samaneh ghassabi kondalaji*
> *PhD student in Chemistry*
> *555 CRL, Chemistry department*
> *West Virginia University *
> *Morgantown, USA*
>
> *E-mail: **saghassabikondalaji.mix.wvu.edu*
> <saghassabikondalaji.mix.wvu.edu>
>
>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 17 2017 - 10:00:03 PDT
