[AMBER] Converting Amoeba .xyz for use with Amber

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Thu, 5 Dec 2013 20:05:09 -0800

Hello Amber community,

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".

Do any of you happen to have successfully ran Amoeba simulations with latest Amber and Tinker? If so, what must I specify in the key file for the conversion to succeed? Or should I just revert to using Tinker 4.3 with amoebapro4?

Thank you,
Eugene Yedvabny
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Received on Thu Dec 05 2013 - 20:30:02 PST
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