Have you worked through the MCPB tutorial yet?
http://ambermd.org/tutorials/advanced/tutorial20/
On Fri, Aug 1, 2014 at 2:17 PM, Pedro A. Baldera Aguayo <
a.baldera7.gmail.com> wrote:
> Hi!
>
> I'm a totally newbie in Amber. I'm facing some problems when trying to
> build the topology files for a Zn metalloprotein, which is connected
> bounded to 3 histidines (I have already from HIS to HID), 1 aspartate and 2
> water molecules. I've tried to following your comments according this post
> http://archive.ambermd.org/201406/0518.html; however:
>
> 1. I do not how to add the Hydrogens to the water molecules via tleap
>
> 2. Do I need to change HOH to MOH for the 2 molecules that are bounded to
> the Zn in order to be recognized for MCPB? Is this mandatory? It is a
> suggestion?
>
> I would really appreciate your help, thanks in advance for your time
>
> Pedro
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 01 2014 - 12:00:02 PDT
