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
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>> 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
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Received on Tue Feb 01 2011 - 09:00:04 PST
