From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Fri Apr 10 2015 - 05:05:42 CDT
Dear all
I have a disulfide bridged cystine molecule in a zwitter ion form, to
remove the charges i have amidated the C-terminal and acetylated the
N-terminal. Now in this pdb i have 38 atoms and the atom names are
according to the Charmm topology file (top_all27_prot_lipid_na.inp),
But, when i am trying to solvate it , it is ignoring the disulfide,
acetylated and amidated patches, and creating the psf file for only 25
atoms (when the resname is CYS). When i am changing the residue names by
the patch names (ACE for acetalaion, CT2 for amidation, and DISU for
disulfide SG and CB) then also it is giving the following error:
"unknown residue type ACE".
The PDB file i have is:
ATOM 1 CAY CYS 14 -4.080 49.790 62.010 0.00 0.00 C
ATOM 2 CY CYS 14 -3.229 48.731 61.503 0.00 0.00
C
ATOM 3 OY CYS 14 -4.021 47.729 60.932 0.00 0.00
O
ATOM 4 N CYS 14 -1.840 48.367 61.392 0.00
0.00 N
ATOM 5 CA CYS 14 -0.992 47.311 60.887 0.00
0.00 C
ATOM 6 1CB CYS 14 -0.081 47.849 59.785 0.00 0.00
C
ATOM 7 1SG CYS 14 0.906 46.497 59.054 0.00 0.00
S
ATOM 8 C CYS 14 -0.176 46.758 62.031 0.00
0.00 C
ATOM 9 NT CYS 14 -0.762 45.707 62.822 0.00
0.00 N
ATOM 10 O CYS 14 0.958 47.176 62.300 0.00
0.00 O
ATOM 11 HT2 CYS 14 -1.681 45.492 62.466 0.00 0.00
H
ATOM 12 HT1 CYS 14 -0.181 44.885 62.771 0.00 0.00
H
ATOM 13 HY1 CYS 14 -3.463 50.570 62.454 0.00 0.00
H
ATOM 14 HY2 CYS 14 -4.662 50.210 61.191 0.00 0.00
H
ATOM 15 HY3 CYS 14 -4.753 49.386 62.764 0.00 0.00
H
ATOM 16 HB1 CYS 14 -0.228 48.923 59.685 0.00 0.00
H
ATOM 17 HB2 CYS 14 0.708 47.657 60.511 0.00 0.00
H
ATOM 18 HN CYS 14 -1.274 49.083 61.800 0.00 0.00
H
ATOM 19 HA CYS 14 -1.591 46.530 60.467 0.00 0.00
H
ATOM 20 2SG CYS 17 2.700 47.388 58.627 0.00 0.00 S
ATOM 21 2CB CYS 17 3.465 47.784 60.221 0.00 0.00 C
ATOM 22 CA CYS 17 4.203 46.620 60.883 0.00 0.00
C
ATOM 23 N CYS 17 3.322 45.484 61.134 0.00
0.00 N
ATOM 24 CY CYS 17 1.945 45.083 61.001 0.00 0.00
C
ATOM 25 CAY CYS 17 1.744 44.469 59.703 0.00 0.00 C
ATOM 26 C CYS 17 4.775 47.153 62.194 0.00
0.00 C
ATOM 27 NT CYS 17 3.916 47.442 63.313 0.00 0.00
N
ATOM 28 O CYS 17 5.993 47.336 62.287 0.00
0.00 O
ATOM 29 OY CYS 17 1.428 44.763 62.262 0.00 0.00
O
ATOM 30 HN CYS 17 3.851 44.734 61.531 0.00 0.00
H
ATOM 31 HA CYS 17 4.974 46.260 60.235 0.00 0.00
H
ATOM 32 HB1 CYS 17 2.655 48.023 60.878 0.00 0.00 H
ATOM 33 HB2 CYS 17 4.215 48.517 60.007 0.00 0.00 H
ATOM 34 HT2 CYS 17 2.961 47.237 63.065 0.00 0.00 H
ATOM 35 HT1 CYS 17 4.470 47.782 64.083 0.00 0.00 H
ATOM 36 HY1 CYS 17 0.704 44.165 59.602 0.00 0.00 H
ATOM 37 HY2 CYS 17 1.397 43.445 59.835 0.00 0.00 H
ATOM 38 HY3 CYS 17 2.388 43.595 59.611 0.00 0.00 H
END
Please someone tell me what changes i should make in the topology file or
in the PDB file.
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
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