Re: [AMBER] TI in vacuum

From: FCUP <Sílvia>
Date: Tue, 1 Feb 2011 17:08:22 +0000

Hi,
the folder was removed.
I am trying to send the pdb file.

Thanks,
Sílvia Martins

No dia 1 de Fevereiro de 2011 17:02, Sílvia Martins (FCUP) <
silvia.martins.fc.up.pt> escreveu:

> Hi,
>
> yes, the simulations work in water, with no problem.
> When I try to run the simulation again, it stops at the same point.
> The final structure looks ok again. I attached a folder with some files.
>
> Thanks again!
>
> Sílvia
>
>
> 2011/2/1 <steinbrt.rci.rutgers.edu>
>
>> do the simulations work in water? Do they stop at the same point each
>> time, or not start at all? What does the final structure look like?
>>
>> Thomas
>>
>> On Tue, February 1, 2011 11:28 am, Sílvia Martins (FCUP) wrote:
>> > The compounds are, for example, Imidazole-->Imidazole-5-ol or
>> > Purine-->Purine-8-ol.
>> >
>> > 2011/2/1 <steinbrt.rci.rutgers.edu>
>> >
>> >> > However, with some compounds, the vacuum simulations stop, without
>> any
>> >> > error
>> >> > message. This occurs in step2, when hidrogen disappears while
>> >> > simultaneously
>> >> > the hydroxyl group appears.
>> >> >
>> >> > What could be the problem?
>> >>
>> >> hm, you are not giving that much information about the problem, so its
>> >> not
>> >> easy to say anything beyond the fact that in principle, TI should work
>> >> in
>> >> vacuum as well. Do your simulations stop at the same point each time?
>> Do
>> >> you see anything in the structure when you write out the trajectory?
>> Did
>> >> you check both output files for errors (sometimes a message only
>> appears
>> >> in v0.out or v1.out)
>> >>
>> >> Regards,
>> >>
>> >> Tom
>> >>
>> >> Dr. Thomas Steinbrecher
>> >> formerly at the
>> >> BioMaps Institute
>> >> Rutgers University
>> >> 610 Taylor Rd.
>> >> Piscataway, NJ 08854
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> > Hi Tom,
>> >
>> > thanks for the quick response.
>> > I can say that this happened,for instance, with these two
>> transformations:
>> > Imidazole-->Imidazole-5-ol or Purine-->Purine-8-ol.
>> >
>> > Do your simulations stop at the same point each time?
>> > Did you check both output files for errors (sometimes a message only
>> > appears
>> > in v0.out or v1.out)
>> >
>> >
>> > In the two examples, in the first one, it stops at lambda=0.4, because
>> the
>> > v0 stops - with no error message - and v1 terminates normally.
>> > With this, a coordinate file (.rst file) is written for v1 but not for
>> v0
>> > and the calculation stops.
>> > In the second transformation, it stops at lambda=0.1, and the v0 stops
>> > with
>> > no error message and v1 terminates normally, again.
>> >
>> > Do you see anything in the structure when you write out the trajectory?
>> >
>> > I am not writing a trajectory file for each lambda. For each lambda, i
>> am
>> > just writing a coordinate file that corresponds to the last structure.
>> > With this, for v0, I have a coordinate file for lambda=0.3 that seems
>> ok.
>> >
>> > Thanks again for your help.
>> > I am available for further explanation if necessary.
>> >
>> > Sílvia Martins
>> >
>> >
>> >
>> >
>> >
>> > --
>> > Sílvia Alexandra Pinto Martins
>> > PhD student
>> > Chemistry Department
>> > Faculty of Sciences
>> > University of Porto
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Dr. Thomas Steinbrecher
>> formerly at the
>> BioMaps Institute
>> Rutgers University
>> 610 Taylor Rd.
>> Piscataway, NJ 08854
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Sílvia Alexandra Pinto Martins
> PhD student
> Chemistry Department
> Faculty of Sciences
> University of Porto
>



-- 
Sílvia Alexandra Pinto Martins
PhD student
Chemistry Department
Faculty of Sciences
University of Porto



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Received on Tue Feb 01 2011 - 09:30:10 PST
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