Re: [AMBER] Converting Amoeba .xyz for use with Amber

From: Jason Swails <>
Date: Fri, 6 Dec 2013 17:11:08 -0500

On Fri, Dec 6, 2013 at 8:27 AM, David A Case <>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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Dec 06 2013 - 14:30:02 PST
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