From: Randy J. Zauhar (r.zauhar_at_usciences.edu)
Date: Fri Sep 06 2013 - 09:40:09 CDT
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
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