From: Sai Kumar Ramadugu (sramadugu_at_gmail.com)
Date: Mon Jan 28 2013 - 13:28:06 CST
Hello NAMD Users,
I downloaded the latest charmmff parameter files for proteins and
carbohydrates from Alex MacKerell's website and when I use VMD to generate
pdb and psf files (from NAMD tutorial),
the writepdb and writepsf commands do not result in any error but for a
mannose disaccharide, there should be only 45 atoms but the writepsf
results in writing 48 atoms which is wrong for a disaccharide.
I am using namd 2.9 and vmd 1.9.1. I tried using psfgen from both vmd and
namd.
I am pasting the output of writepsf command:
psfgen) reading coordinates from pdb file dimannose.pdb for segment U
psfgen) Info: writing psf file dim.psf
psfgen) total of 48 atoms
psfgen) total of 48 bonds
psfgen) total of 84 angles
psfgen) total of 132 dihedrals
psfgen) total of 0 impropers
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file dim.pdb
psfgen) Info: pdb file complete.
The resulting pdb from writepdb:
REMARK original generated coordinate pdb file
ATOM 1 C1 AMAN 1 57.080 18.469 16.504 1.00 0.00
U C
ATOM 2 H1 AMAN 1 57.468 18.100 15.660 1.00 0.00
U H
ATOM 3 O1 AMAN 1 57.765 19.682 16.731 1.00 0.00
U O
ATOM 4 HO1 AMAN 1 58.706 19.513 16.782 1.00 0.00
U H
ATOM 5 C5 AMAN 1 56.975 17.970 18.842 1.00 0.00
U C
ATOM 6 H5 AMAN 1 57.461 18.829 19.003 1.00 0.00
U H
ATOM 7 O5 AMAN 1 57.369 17.547 17.535 1.00 0.00
U O
ATOM 8 C2 AMAN 1 55.561 18.697 16.432 1.00 0.00
U C
ATOM 9 H2 AMAN 1 55.381 19.323 15.673 1.00 0.00
U H
ATOM 10 O2 AMAN 1 54.845 17.513 16.141 1.00 0.00
U O
*ATOM 11 HO2 AMAN 1 0.000 0.000 0.000 -1.00 0.00
U H*
ATOM 12 C3 AMAN 1 55.030 19.165 17.796 1.00 0.00
U C
ATOM 13 H3 AMAN 1 55.356 20.094 17.970 1.00 0.00
U H
ATOM 14 O3 AMAN 1 53.615 19.280 17.791 1.00 0.00
U O
ATOM 15 HO3 AMAN 1 53.370 20.205 17.790 1.00 0.00
U H
ATOM 16 C4 AMAN 1 55.458 18.220 18.922 1.00 0.00
U C
ATOM 17 H4 AMAN 1 54.964 17.351 18.894 1.00 0.00
U H
ATOM 18 O4 AMAN 1 55.080 18.777 20.168 1.00 0.00
U O
ATOM 19 HO4 AMAN 1 54.995 19.726 20.081 1.00 0.00
U H
ATOM 20 C6 AMAN 1 57.392 16.894 19.835 1.00 0.00
U C
ATOM 21 H61 AMAN 1 57.219 17.188 20.775 1.00 0.00
U H
ATOM 22 H62 AMAN 1 56.907 16.037 19.659 1.00 0.00
U H
ATOM 23 O6 AMAN 1 58.772 16.642 19.710 1.00 0.00
U O
ATOM 24 HO6 AMAN 1 58.923 15.697 19.682 1.00 0.00
U H
ATOM 25 C1 AMAN 2 54.771 17.152 14.752 1.00 0.00
U C
ATOM 26 H1 AMAN 2 54.851 17.980 14.196 1.00 0.00
U H
*ATOM 27 O1 AMAN 2 0.000 0.000 0.000 -1.00 0.00
U O
ATOM 28 HO1 AMAN 2 0.000 0.000 0.000 -1.00 0.00
U H*
ATOM 29 C5 AMAN 2 56.084 15.193 15.133 1.00 0.00
U C
ATOM 30 H5 AMAN 2 56.228 15.524 16.066 1.00 0.00
U H
ATOM 31 O5 AMAN 2 55.867 16.356 14.337 1.00 0.00
U O
ATOM 32 C2 AMAN 2 53.481 16.340 14.615 1.00 0.00
U C
ATOM 33 H2 AMAN 2 52.673 16.863 14.886 1.00 0.00
U H
ATOM 34 O2 AMAN 2 53.246 16.052 13.251 1.00 0.00
U O
ATOM 35 HO2 AMAN 2 53.193 15.104 13.129 1.00 0.00
U H
ATOM 36 C3 AMAN 2 53.589 15.063 15.452 1.00 0.00
U C
ATOM 37 H3 AMAN 2 53.598 15.280 16.428 1.00 0.00
U H
ATOM 38 O3 AMAN 2 52.423 14.270 15.311 1.00 0.00
U O
ATOM 39 HO3 AMAN 2 51.653 14.837 15.279 1.00 0.00
U H
ATOM 40 C4 AMAN 2 54.851 14.281 15.091 1.00 0.00
U C
ATOM 41 H4 AMAN 2 54.764 13.852 14.192 1.00 0.00
U H
ATOM 42 O4 AMAN 2 55.006 13.211 15.995 1.00 0.00
U O
ATOM 43 HO4 AMAN 2 55.041 13.551 16.889 1.00 0.00
U H
ATOM 44 C6 AMAN 2 57.327 14.467 14.631 1.00 0.00
U C
ATOM 45 H61 AMAN 2 57.440 13.592 15.102 1.00 0.00
U H
ATOM 46 H62 AMAN 2 57.270 14.310 13.645 1.00 0.00
U H
ATOM 47 O6 AMAN 2 58.489 15.239 14.876 1.00 0.00
U O
ATOM 48 HO6 AMAN 2 59.250 14.661 14.931 1.00 0.00
U H
END
The three additional atoms are highlighted in red with bold font.
Any help will be great.
Thanks and regards
Sai
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:55 CST