VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Wed Mar 19 2014 - 13:07:42 CDT

Hi everybody,

Can somebody share an example of how to use "residue" in psfgen to fill in
amino-acids that are missing in a PDB?

I am working with structure 4HBC. The monomer named H has two serines in
positions 135 and 136 that are missing in the positional information.

This is an excerpt fro the 4HBC.pdb wher you can see that positional
information skips from resid 134 to 137.
...
ATOM 1017 N THR H 133 -60.259 26.798 -21.481 1.00
44.57 N
ATOM 1018 CA THR H 133 -60.887 25.485 -21.267 1.00
51.05 C
ATOM 1019 C THR H 133 -59.916 24.273 -21.475 1.00
54.98 C
ATOM 1020 O THR H 133 -59.389 24.074 -22.579 1.00
57.77 O
ATOM 1021 CB THR H 133 -62.200 25.381 -22.089 1.00
53.68 C
ATOM 1022 OG1 THR H 133 -62.808 24.096 -21.894 1.00
60.25 O
ATOM 1023 CG2 THR H 133 -61.958 25.650 -23.594 1.00
56.91 C
ATOM 1024 N PRO H 134 -59.670 23.473 -20.405 1.00
57.37 N
ATOM 1025 CA PRO H 134 -58.706 22.338 -20.445 1.00
56.94 C
ATOM 1026 C PRO H 134 -59.074 21.172 -21.373 1.00
62.62 C
ATOM 1027 O PRO H 134 -58.254 20.268 -21.584 1.00
62.58 O
ATOM 1028 CB PRO H 134 -58.654 21.855 -18.984 1.00
58.07 C
ATOM 1029 CG PRO H 134 -59.897 22.397 -18.347 1.00
58.81 C
ATOM 1030 CD PRO H 134 -60.205 23.690 -19.044 1.00
50.39 C
ATOM 1031 N THR H 137 -56.064 18.107 -18.639 1.00
50.63 N
ATOM 1032 CA THR H 137 -54.612 18.345 -18.474 1.00
44.58 C
ATOM 1033 C THR H 137 -54.202 19.838 -18.557 1.00
40.24 C
ATOM 1034 O THR H 137 -54.496 20.527 -19.551 1.00
40.54 O
ATOM 1035 CB THR H 137 -53.780 17.473 -19.454 1.00
52.37 C
ATOM 1036 OG1 THR H 137 -52.386 17.754 -19.298 1.00
53.79 O
ATOM 1037 CG2 THR H 137 -54.188 17.709 -20.924 1.00
53.97 C
ATOM 1038 N VAL H 138 -53.514 20.333 -17.524 1.00
31.81 N
ATOM 1039 CA VAL H 138 -53.117 21.759 -17.499 1.00
28.77 C
ATOM 1040 C VAL H 138 -51.619 21.892 -17.199 1.00
26.21 C
ATOM 1041 O VAL H 138 -51.065 21.118 -16.437 1.00
27.01 O
ATOM 1042 CB VAL H 138 -54.025 22.634 -16.556 1.00
29.39 C
ATOM 1043 CG1 VAL H 138 -53.992 22.156 -15.122 1.00
31.74 C
ATOM 1044 CG2 VAL H 138 -53.651 24.114 -16.583 1.00
27.45 C
...

I am trying to figure out how to modify my VMD script to fill in those
missing serines.

At the moment I am only establishing the disulfide bonds and adding the
hydrogen:

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD

segment H {pdb 4HBC_p_H.pdb}
patch DISU H:21 H:92
patch DISU H:142 H:195
patch DISU H:130 H:215
coordpdb 4HBC_p_H.pdb H
guesscoord
writepdb 4HBC_p_H_H.pdb
writepsf 4HBC_p_H_H.psf

quit

I tried inserting the statement

residue 135 SER H

into a number of positions in that script but I consistently get the same
error: "no segment in progress for residue".

Could somebody enlighten me with a proper segment definition?

Thank you,

Ivan

I have a tcl script that takes a protein only pdb file and

Ivan Gregoretti, PhD
Bioinformatics