Please keep emails forwarded to the Amber mailing list instead of just
private emails (I believe you need to "reply-all" to do this).
On Tue, Jul 15, 2014 at 1:00 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear Jason,
>
> Thanks for your reply.
>
> By the way the inter-molecular HB calculation do not include the
> intra-molecular HB. Here is the header from the output file.
>
Careful. Residues are not always the same as molecules. Water is an
exception -- one water residue is one water molecule. But a single protein
"molecule" is often comprised of hundreds of residues (or more). I believe
lipids are broken up into 3 residues by Lipid11 and Lipid14, so there may
very well be intramolecular hydrogen bonds included in your table.
>
> HBOND SUMMARY
> output to file HB_inBothLayers_001_128-bcmLyo25perS.tbl,
> data was sorted, intra-residue interactions are NOT included,
>
> Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
>
> Hydrogen bond information dumped for occupancies > 0.00
>
> DONOR ACCEPTORH ACCEPTOR
> atom# res.atom atom# res.atom atom# res.atom %occupied distance
> angle
> | 11371 109.O13 | 10322 99.H13 10321 99.O13 | 99.80 2.778 (
> 0.12) 21.73 (10.36)
> | 7706 74.O15 | 11684 112.H12 11683 112.O12 | 99.41 2.805 (
> 0.14) 20.68 (10.68)
> | 28 1.O12 | 1499 15.H12 1498 15.O12 | 99.27 2.770 (
> 0.13) 20.87 (10.15)
> | 2548 25.O12 | 2139 21.H16 2138 21.O16 | 99.12 2.827 (
> 0.15) 18.08 ( 9.92)
>
> So keeping this in mind, I had calculated the HB.
>
> Anyway I shall try to use cpptraj from AMBER 14.
>
> By the way, I am little worry about the version of AMBER. Currently I am
> using AMBER12. Now if I install AMBER tools 14 than I may find some
> difficulty in setting up the path for AMBERHOME for using amber12 and
> amber14.
>
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
Basically, AMBERHOME should be set to AmberTools 14, since only AmberTools
requires AMBERHOME be set. Then you can continue to use pmemd and
pmemd.cuda from Amber 12.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 09:00:02 PDT
