Re: Atom indices in collective variable definition

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Sep 06 2013 - 09:56:06 CDT

Hi Randy,

There are actually two options, to try and suit everyone's taste. You may provide a PDB file of the whole system, in which case the colvars will look up atoms by their 1-based number. But in systems with many atoms, PDB files become large and impractical, so you may also provide just the coordinates of the required atoms. Then all coordinates are used in the order of the file, and the numbering is ignored.

The tutorial example uses the second option: the PDB file contains just the right coordinates. The atom numbers are not used to find the reference coordinates in the file, but they define the atom group, ie, which atoms are involved in the RMSD calculation.

Cheers,
Jerome

----- Original Message -----
>
> 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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