Dear Ross,
Thanks for your quick response to clarify this question!
Could you give me one more suggestion?
Does Amber provide any tool or command that can deprotonate / protonate a
protein
or peptide at certain pH ?
thanks,
Tom
On Wed, Jan 27, 2010 at 2:27 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Tom,
>
> You are correct. The charges in the lib file should be those generated from
> the RESP procedure. Gaussian is used to calculate the electrostatic
> potential which is used to fit the charges using RESP. It looks like the
> wrong lib file was uploaded. I never checked this before.
>
> I will update the file to contain the correct charges.
>
> Thanks for spotting this.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Tom Williams
> > Sent: Wednesday, January 27, 2010 1:46 PM
> > To: amber.ambermd.org
> > Subject: [AMBER] Question of Tutorials-A1 about charges compuation from
> > Guassian for Amber
> >
> > I have a question of Amber Tutorials-A1. Anyone can help with this
> > question,
> > thank you!
> > http://ambermd.org/tutorials/advanced/tutorial1/
> >
> > In this tutorial, it seems to me that amber uses the partial charges
> > computed from Gaussian.
> > But i don't know why these values of partial charges computed from
> > Gaussian
> > become
> > totally different after importing to Amber.
> >
> > Pls compare these two file:
> > 1) the result from Guassian computation: Figure 1.4 at
> > http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
> > 2) after manual assigning the type and the partial chage to each atom
> > and
> > generate the file of fam5.lib and fam5_leap.pdb in Section 3.3.1)
> > Saving
> > our new library file
> > http://ambermd.org/tutorials/advanced/tutorial1/section3.htm
> >
> > you also can use xleap to see the charges
> > $AMBERHOME/exe/xleap &
> > loadoff fam5.lib
> > loadamberparams fam5.frcmod
> > FAM = copy FAM5
> > mol = loadpdb fam5_leap.pdb
> > edit mol
> > you can see the charge of atoms
> > They are totally different from the ones shown in Figure 1.4 which are
> > calculated from Gaussian.
> > Can anyone help exlain this? thanks!
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>
>
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Received on Wed Jan 27 2010 - 15:30:02 PST
