Dear dac,
Thanks for prompt reply.
This is link for tutorial
http://ambermd.org/tutorials/basic/tutorial3/section6.htm
http://ambermd.org/tutorials/basic/tutorial3/files/analyse_hbond.ptraj
Regards,
Nitin Sharma
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Wednesday, March 19, 2014 4:16 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Hbond
On Wed, Mar 19, 2014, Nitin Sharma wrote:
>
> 1. In the amber12 tools, as I am using amber12, acceptormask and donormask are the keywords BUT in tutorial they are mentioned as acceptor mask and donor mask. So which one is correct?
>
> 2. To refer a particular atom, like required in case of disulphide
> bond, I used :GLN.OE1 BUT in tutorial it has been mentioned as
> :GLN.OE1. So which one is correct?
The tutorials look wrong...can you say which tutorial (and which section), to help us get those fixed.
>
>
> I know that in Hbond the donor is
> hydrogen bound to electronegative atom and acceptor is a
> electronegative atom present at different location.
YOU know that, and so do most people. But the (unnamed here) author of ptraj, back in prehistory [probably before you were born] chose the opposite convention.
I strongly recommend that you use cpptraj, where a more common definition of donor and acceptor are used.
...dac
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Received on Tue Mar 18 2014 - 22:00:03 PDT
