VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Wed Mar 19 2014 - 17:58:24 CDT

Hi Josh,

Splitting the pdb into nterm.pdb and cterm.pdb does the trick. Thank you.

Now I am trying to figure out a way to do that without splitting the
original file into two. Why? Because in the structures I will be working on
I expect multiple missing amino-acids per monomer. And I will be working
with many structures. I better try not to provoke and explosion of partial
pdb files.

The solution would be (it may not exist) to call the pdb command with a
range, something like

segment H {
pdb 1:134 4HBC_p.pdb
residue 135 SER
residue 136 SER
pdb 137:end 4HBC_p.pdb
}

I do not think that a call to "pdb" offers that option. I will keep trying,
I have no choice honestly.

Thank you

Ivan

Ivan Gregoretti, PhD
Bioinformatics

On Wed, Mar 19, 2014 at 3:01 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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 -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
>
>
>