VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Mar 19 2014 - 14:01:37 CDT

Hi Ivan,

The residue command operates within the segment. For example, this is
what I did for a protein that was missing its N-terminal methionine:

segment EMU {
        residue 1 MET
        pdb 3VVJ-chainA.pdb
}

For your case, I think what would be cleanest would be to make two pdbs,
one containing residues 1 to 134 (call it nterm.pdb), one containing the
rest (call it cterm.pdb), and then do the following:

segment H {
pdb nterm.pdb
residue 135 SER
residue 136 SER
pdb cterm.pdb
}

The coordpdb command can use the original pdb, as I believe psfgen
doesn't count on the residues being contiguous when adding coordinates
to the topology (although I've been known to be wrong in the past).

Good luck!
-Josh Vermaas

On 03/19/2014 01:07 PM, Ivan Gregoretti wrote:
> 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
> <tel:60.259%C2%A0%2026.798> -21.481 1.00 44.57 N
> ATOM 1018 CA THR H 133 -60.887 25.485
> <tel:60.887%C2%A0%2025.485> -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
> <tel:61.958%C2%A0%2025.650> -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
> <tel:58.654%C2%A0%2021.855> -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
> <tel:54.496%C2%A0%2020.527> -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
> <tel:54.188%C2%A0%2017.709> -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
> <tel:51.065%C2%A0%2021.118> -16.437 1.00 27.01 O
> ATOM 1042 CB VAL H 138 -54.025 22.634
> <tel:54.025%C2%A0%2022.634> -16.556 1.00 29.39 C
> ATOM 1043 CG1 VAL H 138 -53.992 22.156
> <tel:53.992%C2%A0%2022.156> -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
>