AMBER Archive (2006)

Subject: AMBER: how to add hydrogen molecules in the protein

From: Rachel (comeonsos_at_googlemail.com)
Date: Thu Oct 26 2006 - 11:28:16 CDT

Hi, all,

Thanks for your replies and now i know how to select those uncorrect
residues.

Now I have another question, I want to add a few hydrogen molecules into my
protein, I want to use the hydrogen model of Hunter et al., which is a three
point molecule with two atoms and a dummy placed at their midpoint, and the
charges for the two hydrogen atoms are 0.475 while it is -0.95 for the
dummy. Anyone can tell me how to do that? also if I want to add for example
100 hydrogen molecules, do i need to use the add command for 100 times?

Best regards,
Rachel

On 10/26/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Dear Rachel,
>
> You might also find the following tutorial helpful:
> http://amber.scripps.edu/tutorials/basic/tutorial2/
>
> See section 8 for details on selecting atoms, bonds etc.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Andres Palencia
> > Sent: Thursday, October 26, 2006 04:57
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: how to select the problematic
> > residues(atoms) in VMD
> >
> > Rachel wrote:
> > > Dear AMBER users,
> > >
> > > Hi! I am using VMD to view the trajectory from AMBER(the *.mdcrd
> > > file), from the movie, I can see some of the bonds became
> > so stretched
> > > (became so far away from the protein), which obviously should not
> > > happen, however, how do I know which bonds are they, which residues
> > > they belong to so that I can look at them in more details? Thanks a
> > > lot for your help.
> > >
> > > Best regards,
> > > Rachel
> > Dear Raquel,
> >
> > just to know which residues are responsible for the H-bonds observed,
> > you should go to mouse option in VMD and click label atom.
> > Then pick on
> > the atom making the bond, and it will give you the atom and
> > the residue
> > belonging to.
> > I f you are new user with VMD this link will be useful for
> > you, I am new
> > user also:
> > http://bioweb.pasteur.fr/docs/doc-gensoft/vmd/vmd_help.html
> >
> > good luck, andres...
> > --------------------------------------------------------------
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>
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