Re: Atom indices in collective variable definition

From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Sep 06 2013 - 09:47:30 CDT

I think in the case of the refpositionsfile, it simply matches 1 for 1 with
your colvar. That is, I think it still works regardless of what the atom
numbering is in the x-ray.pdb, it just takes the first line and assumes
that matches the first atomnumbers entry.

On Fri, Sep 6, 2013 at 10:40 AM, Randy J. Zauhar <r.zauhar_at_usciences.edu>wrote:

> In NAMD documentation, it looks like atom numbers used to define
> collective variables are always "1based", i.e. the atom index in the PDB
> file is ignored. However, in at least one example I see, the "Protein
> Ligand" tutorial (Gumbart, Roux & Chipot), there is a collective variable
> definition like this:
>
> rmsd {
> atoms {
> atomnumbers { 887 893 895 897 901 902 903 907 909 915
> 916 917 919 921 926 927 928 930 932 947
> 948 949 951 953 958 959 960 964 966 972
> 973 974 978 980 986 987 988 992 994 1000
> 1001 1002 1006 1008 1014 1015 1016 1019 1023 1025 }
> }
> refpositionsfile x-ray.pdb
> }
>
> where the reference file x-ray.pdb holds only a portion of the structure,
> and starts like this:
>
> ATOM 887 CAY ALA P 1 13.017 -0.597 7.151 1.00 0.00
> PPRO C
> ATOM 893 N ALA P 1 10.724 -0.703 7.930 1.00 0.00
> PPRO N
> ATOM 895 CA ALA P 1 9.372 -0.236 8.097 1.00 0.00
> PPRO C
> ATOM 897 CB ALA P 1 8.452 -1.433 8.230 1.00 0.00
> PPRO C
>
> Looks like the atom number in the file is being used, not the internal
> NAMD number (per the manual, the first atom should be specified as "1" not
> "837" ). So, what is correct?
>
> Thanks!
>
> Randy
>
> Randy J. Zauhar, PhD
> Assoc. Prof. of Biochemistry
> Director, Graduate Program in Bioinformatics
> Dept. of Chemistry & Biochemistry
> University of the Sciences in Philadelphia
> 600 S. 43rd Street
> Philadelphia, PA 19104
>
> Phone: (215)596-8691
> FAX: (215)596-8543
> E-mail: r.zauhar_at_usp.edu<mailto:r.zauhar_at_usp.edu>
> Web: http://binfcompsci.usp.edu/~zauhar
>
>
>
> "The blunt, pathetic reality today is that a little old lady has died, who
> in the winter of her life had to water roses alone under police
> supervision. If you behave like there's no such thing as society, in the
> end there isn't. "
>
> -- Russell Brand on Margaret Thatcher
>
>
>
>
>
>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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