Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: 冉挺 <>
Date: Thu, 3 Oct 2013 21:07:40 +0800

Dear Prof. David,

That's kind for your answer.My test run was successful. But I am still
confused by the TI simulation on some respects.

In my mind, I use the miniminzed structure to produce and and then run TI simulation respectively, is that right? or should I
use the two unminimized structure and to minimized first
respectively and then run TI simulation respectively.

 In addition, I suppose TI simulation should be run after the molecular
system has been heated and reachs the equlibrium state, so if all lamda
window TI simulations can be carried out based on the same equilibrated rst

Best Wishes!

On Wed, Oct 2, 2013 at 7:39 PM, David A Case <>wrote:

> On Wed, Oct 02, 2013, 冉挺 wrote:
> > WARNING: Local coordinate 1 differs from partner coordinate
> 1 !
> The starting coordinates for the two systems in TI need to be exactly the
> same. If you can't see why this happening by just looking at the input
> files,
> you may need to expand the error message to print out exactly which
> coordinates are being compared, so that you can see why you are getting
> these
> messages.
> >
> > In V1 state, Residue 136 (is a WAT) was removed in the, but other
> > atoms are with the same coordinate and the same order to
> The program doesn't agree with this statement, and things that correponding
> atoms do not have the same coordinates. You need to figure out why.
> ...dac
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> AMBER mailing list

PhD Ting Ran
Molecular-Design &  Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
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Received on Thu Oct 03 2013 - 06:30:07 PDT
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