[gmx-users] How to calculate radial distribution functions when atoms in different amino acids are named similarly

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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