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 V0.top and
V1.top and then run TI simulation respectively, is that right? or should I
use the two unminimized structure V0.top and V1.top 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
file?
Best Wishes!
On Wed, Oct 2, 2013 at 7:39 PM, David A Case <case.biomaps.rutgers.edu>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 V1.top, but other
> > atoms are with the same coordinate and the same order to V0.top.
>
> 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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--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design & Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Thu Oct 03 2013 - 06:30:07 PDT
