[gmx-users] TWO AMINOACIDS WITH SAME NUMBER IN .GRO FILE

[Justin Lemkul]

On 10/16/14 8:13 AM, Michetti Davide wrote:
> Dear gmx users,
> I have just realized, at the end of a molecular dynamics simulation, that I had in my .gro file to aminoacids with the same number. This happened cause in my pdb file, what was supposed to be residue 53, was instead 52A (due to an insertion of Lys in that position, compared to other homologs). Those are the lines in the .pdb I am talking about.
>
> ATOM    482  HA  ASN A  52      11.594  -3.380  37.114  1.00  0.00           H
> ATOM    483  HB3 ASN A  52      10.188  -5.588  35.526  1.00  0.00           H
> ATOM    484  HB2 ASN A  52      11.571  -5.800  36.555  1.00  0.00           H
> ATOM    485 HD21 ASN A  52       7.924  -5.965  38.224  1.00  0.00           H
> ATOM    486 HD22 ASN A  52       8.207  -5.978  36.494  1.00  0.00           H
> ATOM    487  N   LYS A  52A     11.898  -2.478  34.227  1.00 26.03           N
> ATOM    488  CA  LYS A  52A     12.656  -2.134  33.020  1.00 26.03           C
> ATOM    489  C   LYS A  52A     12.428  -3.160  31.890  1.00 25.58           C
> ATOM    490  O   LYS A  52A     13.333  -3.399  31.090  1.00 25.54           O
> ATOM    491  CB  LYS A  52A     14.147  -1.837  33.318  1.00 26.46           C
>
> So basically in the .gro file the residue 52 is composed by the ASN 52 and LYS 52. The question is if this can constitute a problem for the simulation? It seems that everything went smooth and I got no error, but I would like to double check..
>

mdrun doesn't care about residue numbers at all.

-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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