Hi,
As it states in the manual, the 'donormask' etc keywords do *not* do
any automatic searching for you. When these are specified cpptraj will
use every atom specified (except it will not consider 'H' atoms as
donors ever and will skip over them, which is probably where the
discrepancy you are seeing comes from). To use these masks you should
have specific atoms/residues in mind, e.g. "acceptormask :ASN.O=",
etc. Also keep in mind that if you just use 'donormask' it will
automatically look for hydrogens bonded to the atoms in the mask and
use those as the H atoms; if you specify 'donorhmask' as well there
needs to be a 1 to 1 correspondence between the atoms in 'donormask'
and 'donorhmask'. I suspect you might get results that you want by
simply specifying something like:
hbond :323-337 dist 3.0 angle -1.0 out ncontact.dat avgout
avgcontact.dat nointramol
I strongly recommend you read the entire manual entry for 'hbond' and
understand what each keyword does; it can be a fairly complex command.
-Dan
On Tue, Aug 2, 2016 at 6:50 AM, Sidhu, Khushwant (Dr.)
<k.sidhu.leicester.ac.uk> wrote:
> Hi,
>
> I’m a bit confused with the Hbond command.
> I’m looking for close contacts between a piece of RNA (residues 323-337) and the protein (1-318).
>
> I’m using the following Hbond command (based on a suggestion on this list)
>
> hbond donormask :323-337 donorhmask :323-337 acceptormask :1-318 dist 3.0 angle -1.0 out ncontact.dat argot avgcontact.dat
>
> I get the following output:
>
> #Acceptor DonorH Donor Frames Frac AvgDist AvgAng
> ASN_55.H C_326.OP2 C_327.O2 540 0.6750 2.2852 11.1719
> ASN_55.H C_326.OP1 C_327.C2 534 0.6675 2.5507 11.4750
> ASN_55.H C_326.P C_327.N3 522 0.6525 2.2418 9.7082
> LYS_54.HA C_326.OP2 C_327.O2 397 0.4963 2.6851 9.4948
> ASN_55.HB2 C_325.C6 C_326.O2 377 0.4713 2.7258 9.8223
> ASN_55.HB2 C_326.P C_327.N3 364 0.4550 2.7809 15.4365
> ASN_55.HD22 C_325.H5 C_326.O2' 299 0.3738 2.1425 6.6522
> LYS_57.NZ C_324.O3' C_326.OP1 285 0.3563 2.8193 13.4472
> ASN_55.HB3 C_325.C6 C_326.O2 283 0.3538 2.7656 8.0737
> ASN_55.HB2 C_326.OP1 C_327.C2 279 0.3488 2.7948 14.1744
> ASN_55.HD22 C_325.C6 C_326.O2 262 0.3275 2.0512 4.3175
> ….
> ….
>
> My question is why are the donorH and donor residues different in every case. ?
> Is there a better way to get this information ?
>
> Regards
>
> Sid
> ------------------------------------------------------------------------------------
>
> Dr Khushwant Sidhu
> Senior Experimental Officer / I. T. Professional
>
> Department of Molecular and Cell Biology,
> 1/61 Henry Wellcome Building , University of Leicester,
> Lancaster Road,
> Leicester,
> LE1 7RH
>
> T: 0116 229 7237
> E: k.sidhu.le.ac.uk
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 02 2016 - 09:00:03 PDT
