I'm not sure what name phenix or ccp4 like, but looking in
$CNS_TOPPAR/dna-rna.top, I see this line:
ATOM C5A TYPE=CC3E CHARGE=0.00 END
so CNS likes C5A. If you want CNS to play well with other programs,
just change that line in your topology file to
ATOM C7 TYPE=CC3E CHARGE=0.00 END
or whatever you want.
kmj
On 11/1/08 8:13 PM, Raja Dey wrote:
Dear Friends,
I am tired of renaming an atom name every time I want to switch
among the programs cns, phenix and ccp4 particularly for a carbon atom
C5A of Thymine given below. What name I should give to this atom
specially for cns? Is it C7 or C5A or C5M?
ATOM 1541 P THY K 5 -33.604 -2.379 -7.017 1.00293.90
K P
ATOM 1542 O1P THY K 5 -33.190 -3.005 -5.747 1.00305.95
K O
ATOM 1543 O2P THY K 5 -33.393 -3.107 -8.289 1.00298.26
K O
ATOM 1544 O5' THY K 5 -32.867 -0.964 -7.135 1.00278.14
K O
ATOM 1545 N1 THY K 5 -32.261 0.951 -3.645 1.00297.58
K N
ATOM 1546 C6 THY K 5 -32.334 -0.383 -3.282 1.00295.41
K C
ATOM 1547 C2 THY K 5 -33.001 1.906 -2.968 1.00292.90
K C
ATOM 1548 O2 THY K 5 -32.983 3.098 -3.232 1.00291.97
K O
ATOM 1549 N3 THY K 5 -33.786 1.406 -1.958 1.00289.04
K N
ATOM 1550 C4 THY K 5 -33.903 0.087 -1.558 1.00286.25
K C
ATOM 1551 O4 THY K 5 -34.635 -0.264 -0.640 1.00287.39
K O
ATOM 1552 C5 THY K 5 -33.104 -0.855 -2.294 1.00284.89
K C
ATOM 1553 C5A THY K 5 -33.151 -2.313 -1.950 1.00269.91
K C
ATOM 1554 C2' THY K 5 -30.072 0.525 -4.886 1.00288.00
K C
ATOM 1555 C5' THY K 5 -31.443 -0.886 -7.113 1.00269.59
K C
ATOM 1556 C4' THY K 5 -31.054 0.568 -6.965 1.00273.61
K C
ATOM 1557 O4' THY K 5 -31.989 1.179 -6.040 1.00282.58
K O
ATOM 1558 C1' THY K 5 -31.349 1.354 -4.783 1.00292.39
K C
ATOM 1559 C3' THY K 5 -29.708 0.843 -6.325 1.00277.20
K C
ATOM 1560 O3' THY K 5 -29.453 2.227 -6.477 1.00283.69
K O
Is there any common name of this atom which can be used for all the
programs?
Thanks for any suggestion.
Raja
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