[AMBER] HBond command

From: Sidhu, Khushwant (Dr.) <"Sidhu,>
Date: Tue, 2 Aug 2016 12:50:08 +0000

Hi,

Iím a bit confused with the Hbond command.
Iím looking for close contacts between a piece of RNA (residues 323-337) and the protein (1-318).

Iím 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
Ö.
Ö.

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Aug 02 2016 - 06:00:03 PDT
Custom Search