Re: [AMBER] charge derivation

From: Abelak, Kavin <kabelak.rvc.ac.uk>
Date: Tue, 23 Feb 2016 15:48:51 +0000

You’re quire right about R.E.D. Server - I was being blind and led astray by the numerous “Cannot run Java applet” security prompts and thus had failed to use it previously.

Thanks,
Kavin



> On 19 Feb 2016, at 17:24, David A Case <david.case.rutgers.edu> wrote:
>
> On Fri, Feb 19, 2016, Abelak, Kavin wrote:
>>
>> I find myself needing to derive charges for some non-standard
>> ligands. I’ve had a brief search through the archives
>> and tutorials, and keep getting referred to tutorial A1
>> (http://ambermd.org/tutorials/advanced/tutorial1/section1.htm). Is this
>> still the currently accepted method for running charge derivations using
>> Gaussian? I only ask as it is dated 2008 and cites Amber 10 (and older).
>
> The standard charge derivation procedure has not changed since forever (i.e.
> since the early 1990's). So the tutorial should still be OK, but be sure to
> read the caveat there (in bold type).
>
>>
>> Another related question is: are there other streamlined methods
>> (similar to R.E.D Tools) that anyone can suggest?
>
> Why not use R.E.D. Tools itself? That is the most popular way, as far as I
> can tell. They maintain a large-ish database that may already have your
> ligand, or something close to it.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

[RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> [Facebook icon - link to RVC (Official) Facebook] <http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> [Instagram icon - link to RVC Instagram] <http://instagram.com/royalvetcollege>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 23 2016 - 08:00:04 PST
Custom Search