AMBER Archive (2007)

Subject: Re: AMBER: RESP charge fitting using antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Dec 31 2007 - 08:06:34 CST

Quoting snoze pa <snoze.pa_at_gmail.com>:

> Thanks a lot FyD, I will follow your instructions and request the
> supervisor.

Thanks for pointing me out that the R.E.D. registration procedure
described on the R.E.D. web site was not that obvious. I just updated
the register, getmyinfo & download pages. I added explanations (in red
color) about the license agreements. I hope this makes the whole
registration procedure more "understandable"...

regards, Francois

> On Dec 30, 2007 2:17 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
>> > FyD, but we can not download any of your scripts. These are not for
>> > students, only for PI's. PI's are busy in grant writing not in
>> > configuring RESP charges. > Is it possible for students to download red.
>>
>> I do not agree. I think you simply did not understand the R.E.D.
>> registration procedure ;-)
>>
>> The PI registers herself/himself, i.e. provides the information
>> requested for the registration. Then, once the PI has registered, all
>> her/his post-docs/students can use R.E.D. & its related tools.
>>
>> This means ask YOUR BOSS to register, and YOU and other
>> students/post-doc belonging to the lab of YOUR BOSS will be able to
>> use R.E.D.
>>
>> regards, Francois
>>
>> PS I am going to modify the web site to make this more obvious.
>>
>> >> Quoting Wei Chen <cwbluesky_at_gmail.com>:
>> >>
>> >> > I need to prepare a .prep file for a non-standard amino acid residue.
>> >> > I followed the procedure in the tutorial
>> >> > http://amber.scripps.edu/antechamber/pro4.html. As a test, I
>> >> > generated a
>> >> > ACE-VAL-NME tripeptide. Going through all steps with antechamber and
>> >> > gaussian 03, I get a prep file for Valine. However, the charge of
>> >> > each atom
>> >> > is quite different from that in all_amino03.in. Could anybody tell me
>> >> > what the reason is?
>> >>
>> >> You could also look at the tutorials @
>> >> http://q4md-forcefieldtools.org/Tutorial/
>> >>
>> >> First of all, charge values in the AMBER force fields are not
>> >> reproducible:
>> >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
>> >> & in particular the section:
>> >> "General information about molecular orientation and charge values"
>> >>
>> >> For information about the Duan et al. FF see:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
>> >>
>> >> To compute charge values for central & terminal fragments see:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11

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