On 8/26/16 9:37 AM, Apramita Chand wrote:
Dear All,
Following is a portion of my .top file showing the naming of atoms of two
of my amino acids of my protein
residue 22 TYR rtp TYR q +1.0
1 NL 22 TYR N 1 0.129 14.0067 ;
qtot 0.129
2 H 22 TYR H1 1 0.248 1.008 ;
qtot 0.377
3 H 22 TYR H2 1 0.248 1.008 ;
qtot 0.625
4 H 22 TYR H3 1 0.248 1.008 ;
qtot 0.873
5 CH1 22 TYR CA 2 0.127 13.019 ;
qtot 1
6 CH2 22 TYR CB 2 0 14.027 ;
qtot 1
7 C 22 TYR CG 2 0 12.011 ;
qtot 1
8 C 22 TYR CD1 3 -0.14 12.011 ;
qtot 0.86
9 HC 22 TYR HD1 3 0.14 1.008 ;
qtot 1
10 C 22 TYR CD2 4 -0.14 12.011 ;
qtot 0.86
11 HC 22 TYR HD2 4 0.14 1.008 ;
qtot 1
12 C 22 TYR CE1 5 -0.14 12.011 ;
qtot 0.86
13 HC 22 TYR HE1 5 0.14 1.008 ;
qtot 1
14 C 22 TYR CE2 6 -0.14 12.011 ;
qtot 0.86
15 HC 22 TYR HE2 6 0.14 1.008 ;
qtot 1
16 C 22 TYR CZ 7 0.203 12.011 ;
qtot 1.203
17 OA 22 TYR OH 7 -0.611 15.9994 ;
qtot 0.592
18 H 22 TYR HH 7 0.408 1.008 ;
qtot 1
19 C 22 TYR C 8 0.45 12.011 ;
qtot 1.45
20 O 22 TYR O 8 -0.45 15.9994 ;
qtot 1
; residue 23 GLY rtp GLY q 0.0
21 N 23 GLY N 9 -0.31 14.0067 ;
qtot 0.69
22 H 23 GLY H 9 0.31 1.008 ;
qtot 1
23 CH2 23 GLY CA 10 0 14.027 ;
qtot 1
24 C 23 GLY C 11 0.45 12.011 ;
qtot 1.45
25 O 23 GLY O 11 -0.45 15.9994 ;
qtot 1
As you can notice , atoms N,C,O of TYR and GLY are named similarly. So when
we calculate rdfs of the protein sites with water molecules, the index
files have to be created which may cause confusion as to which site is
referred to when we mention 'N' or 'C'.
So is re-naming the names necessary or is there a way to calculate rdfs
with the existing file?
Could different index files help? How can we create such index files for
different amino acids?
Specify residue name(s) or number(s) when creating the index group(s).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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