On Fri, Dec 6, 2013 at 8:27 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Dec 05, 2013, Eugene Yedvabny wrote:
> >
> > I am trying to figure out how to convert a Tinker 6.2 inputs (.analout
> > and .xyz) to Amber prmtop/inpcrd with the least headache. I am trying to
> > simulate a small NVE system with no solvent, which means no thermostat
> > or periodic conditions. The tinker_to_amber code, however, does not seem
> > very robust to differences in .analout files: it dies if I don't specify
> > an a-axis or if I omit any of the Amoeba components, such as 'mpoleterm
> > none'. I am using amoebapro13.prm as my parameter file.
> >
> > According to this wiki, I no longer need to use Tinker 4.3 or swap
> > analyze.f, but I am still having a lot of issues getting the conversion
> > to complete. Without omitting any of the Amoeba components, the
> > conversion dies at "wrong number of fields in multipole line: numf =
> > 5".
>
> It's certainly true that tinker_to_amber relies on certain characteristics
> of
> the analout file. However, every analout file I have seen has either 6 or
> 7 fields in the multipole section, whereas you seem to have an example with
> just 5 fields.
>
> We are in the process of trying to update (and better document!) the
> conversion from tinker to amber. (I'm not sure if Jason knows anything
> here
> or not). Could you send your examples that don't work? We'll try to
> figure
> out what is going on.
>
My (far fewer) experiences have been the same -- I've never seen an
"analout" file fail with tinker_to_amber... I think we would need to be
able to reproduce the problem in order to help debug it.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 06 2013 - 14:30:02 PST
