Re: [AMBER] Failed to merge the protein-ligand amoeba parameters

From: David A Case <>
Date: Wed, 28 Nov 2018 07:43:48 -0500

On Tue, Nov 27, 2018, 王茜茜 wrote:

> Recently, I want to test the polariable-force-field simulation for a
>protein-ligand complex. Using Poltype, I obtained the lig.key and
>Using tinker_to_amber, I obtained the prot_solv.prmtop, prot_solv.inpcrd,
>prot_solv.key and (with amoebapro13). Importantly, both of
>them works well by checking "analyze -k X.key ep".
> To build com_solv.prmtop and com_sol.inpcrd, I further merged the .xyz
>files of protein and ligand using "xyzedit", and meanwhile append the
>lig.key into prot.key to obtain the com.key. But when checking "analyze
> -k com.key ep", it gave the wrong information below:
> MECHANIC -- Some Required Potential Energy Parameters are Undefined
> TINKER is Unable to Continue; Terminating the Current Calculation
> Maybe it's the problem of com.key, but the tutorial told to just append
>the prot.key into lig.key. I donnot know how to solve it. And to build the
>complex system, whether what I did are right or not? Any reply will be
>grateful. Thank you.

Thanks for your email. A couple of points, that may be of more general
interest to Amber users:

1. The detailed problem ("TINKER is Unable to Continue") is really a
Tinker issue, and you may wish to ask your question of the tinker

2. More generally: support in Amber for Amoeba calculations is waning.
Basically, Tinker itself, and the OpenMM implementation of Amoeba, have
made so much progress in recent years, that there seems to be little
need for a separate implementation in Amber. We no longer distribute
pmemd.amoeba, for example.

Once you go through all the steps of creating the system in Tinker, it
now probably makes the most sense to continue in Tinker or OpenMM.
While we will do our best to answer questions, my guess is that very few
people use Amber to run Amoeba simulations any more; maybe someone on
the list can prove me wrong! The Tinker/OpenMM approaches, on the other
hand, and both actively developed and more widely used.

[There may be a rejuvenation of interest in the Amber development
community in polarizable force fields, but that will come from
developers wanting to run such simulations, not from a desire to
check-off something on a "list of features".]

Sorry I can't be of more help. I recognize the problem, but haven't
myself worked in that area for several years.


AMBER mailing list
Received on Wed Nov 28 2018 - 05:00:03 PST
Custom Search