Dear Amber users:
I have to map one prep file to another prep file with the same
atom order. But I am not
clear about the meaning of each column of the prep file. Could anybody
explain to me?
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C26 ca M 3 2 1 1.540 111.208 180.000
-0.101200
5 H24 ha E 4 3 2 1.080 76.455 -25.735
0.108400
6 C27 ca S 4 3 2 1.394 65.190 107.332
-0.121500
7 H25 ha E 6 4 3 1.080 118.796 -53.517
0.113700
8 C25 ca M 4 3 2 1.385 131.007 -144.303
-0.097000
9 H23 ha E 8 4 3 1.080 120.015 97.374
0.102400
...................................................................................................
3rd column: atom types
4th column: tree symbol
last column: atom charge
What are columns 5th ~ 7th? Is column 8th bond length? 9th angles? 10th
dihedrals?
If I want to map one file to another, I have to make the columns 5th ~ 7th
the same as the reference?
Many thanks in advance.
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Tue Nov 06 2012 - 14:30:02 PST
