Re: [AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Fri, 1 Aug 2014 15:13:27 -0500

Hi Jason,

Thanks again for your answer. Yes, the water molecules are part of the
metal complexes and what I did was following either MCPT or Pengfei's
tutorial, and in the 2nd step, after typing:

MCPB -i 3PL1_OH_addHs.bcl -l 3PL1_OH_addHs.bcl.log

I got this message

1 Error in watProtonate ... exiting
terminate called after throwing an instance of 'MTKpp::MTKException'
Aborted (core dumped)

And the message in the corresponding log file is:

 ### ### ### ###
 ### MTK++ Info ###
 ### Function: watProtonate::run ###
 ### Message: sorted water energies
 ### ### ### ###

If you have any comments about this, please let me know. Of course, I'm
still waiting for Pengfei because I think that he has already handled this
in a previous post.

Best,

Pedro


2014-08-01 14:27 GMT-05:00 Jason Swails <jason.swails.gmail.com>:

> On Fri, Aug 1, 2014 at 2:38 PM, Pedro A. Baldera Aguayo <
> a.baldera7.gmail.com> wrote:
>
> > Yes, I did. However, I am facing problems with the wster molecules, and I
> > do not how to deal with them.
> >
>
> ‚ÄčIf the water molecules are part of the metal complex, then I think that
> MCPB should have added the necessary hydrogens in one of the steps (or at
> least there was a step to do so, if I recall correctly).
>
> If it's just a "typical" water molecule that is part of the bulk solvent
> (or exchanges with the bulk solvent), then tleap should add those
> automatically, assuming that the water residue is named correctly.
>
> Since I'm not super familiar with MCPB, I'll let Pengfei provide more
> detailed answers if they're needed.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Pedro A. Baldera-Aguayo
National University of Engineering (UNI)
Lima - Peru
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Received on Fri Aug 01 2014 - 13:30:03 PDT
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