Dear GROMACS users and developers,
Sorry for posting same topic again. I really appreciate those replies, thank
you. I did use the -res option so i can get the plot rmsf (nm) vs
residue. However, with -res option, the bfac.pdb produced include the ANISOU
line for each atom (whish is the anistropic temperature factor). The B-factor
is still at the end of each atom line.
My question is, how can I calculate the average of each residue? here's few
line i took form the bfac.pdb:TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 90.072 90.010 90.061 70.58 109.50 70.49 P 1 1
MODEL 1
ATOM 1 N ALA 1 39.870 49.598 31.575 1.00 0.00
ANISOU 1 N ALA 1 27382 16872 28413 -5818 -15784 -6247
ATOM 2 H1 ALA 1 40.270 50.118 30.815 1.00 0.00
ANISOU 2 H1 ALA 1 36121 21080 32250 -8317 -17149 -8021
ATOM 3 H2 ALA 1 40.080 48.628 31.485 1.00 221.02
ANISOU 3 H2 ALA 1 32407 19879 31690 -6481 -17864 -7202ATOM
4 H3 ALA 1 38.870 49.728 31.575 1.00 218.06
ANISOU 4 H3 ALA 1 33154 18573 31125 -6794 -16678 -6289
ATOM 5 CA ALA 1 40.500 50.098 32.805 1.00 168.66
ANISOU 5 CA ALA 1 17671 18590 27822 -3239 -12795 -8333
ATOM 6 CB ALA 1 39.990 49.098 33.845 1.00 220.77
ANISOU 6 CB ALA 1 15699 36171 32009 -10813 -7176 -10100
Can I just average the (B-factor) value at each end of atom line for each
residue?
Its okay if the B-factor vs redisue plot cant be build. I can use the B-factor
vs atoms plot. But people (in papers) have done it (B-fac vs res) before with
GROMACS and I'm eager to see the plot for my protein :)
"May the Force Fields be with You" - GROMACS Wars
Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIAComments, advices and suggestions are greatly appreciated. Thank You.
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