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

From: 王茜茜 <>
Date: Wed, 28 Nov 2018 21:38:18 +0800

Dear Case,
     Thank you very much for the detailed introduction and suggestions.
Since I am familiar with Amber, I initially considered to achieve the
polariable simulations using Amber/Tinker. Indeed, the Tinker/OpenMM
approach was reported widely, so maybe I need to learn them if pmemd.amoeba
will not be distributed. No matter, thanks for your kindly replies very


David A Case <> 于2018年11月28日周三 下午8:44写道:

> 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
> developers.
> 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.
> ....dac
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Received on Wed Nov 28 2018 - 06:00:04 PST
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