VMD-L Mailing List

From: Francesco Greco (francesco.greco_at_chimfarm.unipg.it)
Date: Wed Jun 08 2016 - 07:52:42 CDT

Hi everybody,

I'm writing to understand where is the error in my psfgen script.
Everything seems right, but when autopsf files are written, there are some
additional atoms in the ligand segment (with 0,0,0 coordinates). the ligand
is named "PIM" and the segment is the "T" one.
The single segment is perfect if I visualize it. But in the final file I
have additional atoms (both in psf and pdb output).

The script is:

# (1) Split input PDB file into segments}
cat complex.pdb | egrep
"ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|HSD|ILE|LEU|LYS|MET|PHE|PRO|SER|TYR|THR|VAL"
> output/protein.pdb
cat complex.pdb | grep HEM complex.pdb > output/HEME.pdb
cat complex.pdb | grep PIM complex.pdb > output/PIM.pdb

# (2) Embed the psfgen commands in this script
autopsf << ENDMOL

# (3) Read topology file
topology /home/francesco-g/parameterstocombine/rtf/top_all36_prot.rtf
topology /home/francesco-g/parameterstocombine/rtf/top_all36_HEME.rtf
topology /home/francesco-g/parameterstocombine/rtf/top_PIM.rtf
topology /home/francesco-g/parameterstocombine/rtf/top_water_ions.rtf
topology /home/francesco-g/parameterstocombine/rtf/top_all36_cgenff.rtf
# (4a) Build protein segment
segment P { pdb output/protein.pdb }
# (4b) Build HEME segment
segment O { pdb output/HEME.pdb }
# (4c) Build PIM segment
segment T { pdb output/PIM.pdb }
# (5) Patch protein segment
patch FHEM O:404
patch PHEM P:346 O:404

# (6) Read protein, HEME and PIM coordinates from PDB file
coordpdb output/protein.pdb P
coordpdb output/HEME.pdb O
coordpdb output/PIM.pdb T
# (9) Guess missing coordinates
guesscoord
# (10) Write structure and coordinate files
writepsf output/autopsf.psf
writepdb output/autopsf.pdb

quit

The output of PIM.pdb is:

HETATM 6292 C1 PIM 1 56.259 52.810 17.749 1.00
0.00 C
HETATM 6293 C2 PIM 1 57.229 53.434 16.949 1.00
0.00 C
HETATM 6294 C3 PIM 1 58.551 53.534 17.402 1.00
0.00 C
HETATM 6295 C4 PIM 1 58.905 53.074 18.687 1.00
0.00 C
HETATM 6296 C5 PIM 1 57.921 52.452 19.491 1.00
0.00 C
HETATM 6297 C6 PIM 1 56.603 52.312 19.018 1.00
0.00 C
HETATM 6298 C7 PIM 1 60.271 53.251 19.153 1.00
0.00 C
HETATM 6299 C8 PIM 1 61.418 53.614 18.484 1.00
0.00 C
HETATM 6300 N1 PIM 1 62.504 53.531 19.349 1.00
0.00 N
HETATM 6301 C9 PIM 1 61.973 53.204 20.521 1.00
0.00 C
HETATM 6302 N2 PIM 1 60.647 53.073 20.474 1.00
0.00 N
HETATM 6303 H1 PIM 1 55.244 52.732 17.391 1.00
0.00 H
HETATM 6304 H2 PIM 1 56.968 53.832 15.979 1.00
0.00 H
HETATM 6305 H3 PIM 1 59.283 54.013 16.765 1.00
0.00 H
HETATM 6306 H4 PIM 1 58.168 52.074 20.474 1.00
0.00 H
HETATM 6307 H5 PIM 1 55.854 51.836 19.633 1.00
0.00 H
HETATM 6308 H6 PIM 1 61.558 53.872 17.444 1.00
0.00 H
HETATM 6309 H7 PIM 1 62.558 53.051 21.418 1.00
0.00 H
HETATM 6310 H8 PIM 1 60.048 52.806 21.243 1.00
0.00 H

The output of PIM in autopsf.pdb is:

ATOM 6172 C PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6173 OT1 PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6174 OT2 PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6175 N PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6176 HT1 PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6177 HT2 PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6178 HT3 PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6179 CA PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6180 HA PIM 1 0.000 0.000 0.000 -1.00 0.00
T
ATOM 6181 C1 PIM 1 56.259 52.810 17.749 1.00 0.00
T C
ATOM 6182 C2 PIM 1 57.229 53.434 16.949 1.00 0.00
T C
ATOM 6183 C3 PIM 1 58.551 53.534 17.402 1.00 0.00
T C
ATOM 6184 C4 PIM 1 58.905 53.074 18.687 1.00 0.00
T C
ATOM 6185 C5 PIM 1 57.921 52.452 19.491 1.00 0.00
T C
ATOM 6186 C6 PIM 1 56.603 52.312 19.018 1.00 0.00
T C
ATOM 6187 C7 PIM 1 60.271 53.251 19.153 1.00 0.00
T C
ATOM 6188 C8 PIM 1 61.418 53.614 18.484 1.00 0.00
T C
ATOM 6189 N1 PIM 1 62.504 53.531 19.349 1.00 0.00
T N
ATOM 6190 C9 PIM 1 61.973 53.204 20.521 1.00 0.00
T C
ATOM 6191 N2 PIM 1 60.647 53.073 20.474 1.00 0.00
T N
ATOM 6192 H1 PIM 1 55.244 52.732 17.391 1.00 0.00
T H
ATOM 6193 H2 PIM 1 56.968 53.832 15.979 1.00 0.00
T H
ATOM 6194 H3 PIM 1 59.283 54.013 16.765 1.00 0.00
T H
ATOM 6195 H4 PIM 1 58.168 52.074 20.474 1.00 0.00
T H
ATOM 6196 H5 PIM 1 55.854 51.836 19.633 1.00 0.00
T H
ATOM 6197 H6 PIM 1 61.558 53.872 17.444 1.00 0.00
T H
ATOM 6198 H7 PIM 1 62.558 53.051 21.418 1.00 0.00
T H
ATOM 6199 H8 PIM 1 60.048 52.806 21.243 1.00 0.00
T H

The rest seems ok.

Where is my mistake?

Thank you very much.

Francesco