VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Thu Mar 26 2015 - 10:59:07 CDT

Hello,
I think I have might be similar problem. I have to create pdb and spf files of one metallo chaperon (code 1fd8). The problem is that neither autospf nor spfgen want create spf files. I followed procedure written in namd tutorial but nothing. I just succeeded to wrote files for protein but not for whole molecule including metal (Cu). spfgen usually reports an error (selecting “all”) concerning CTERM end of the protein (LEU 73) that means it found missing N and O atoms (whats not possible). When selected just protein the spfgen behave normally.

I entered CU1 rsesidue into top file:

RESIDUE CU1 -1.0 ! note: this atx1 copper
GROUP ! parameterized charge
ATOM CU Cu 0.15000

END

This is the start and the end of my pdb file:

START
                      .........................
REMARK 900 METALLOCHAPERONE PROTEIN AT 1.02 A RESOLUTION
DBREF 1FD8 A 1 73 UNP P38636 ATX1_YEAST 1 73
SEQRES 1 A 73 MET ALA GLU ILE LYS HIS TYR GLN PHE ASN VAL VAL MET
SEQRES 2 A 73 THR CYS SER GLY CYS SER GLY ALA VAL ASN LYS VAL LEU
SEQRES 3 A 73 THR LYS LEU GLU PRO ASP VAL SER LYS ILE ASP ILE SER
SEQRES 4 A 73 LEU GLU LYS GLN LEU VAL ASP VAL TYR THR THR LEU PRO
SEQRES 5 A 73 TYR ASP PHE ILE LEU GLU LYS ILE LYS LYS THR GLY LYS
SEQRES 6 A 73 GLU VAL ARG SER GLY LYS GLN LEU
HET CU1 A 74 1
HETNAM CU1 COPPER (I) ION
FORMUL 2 CU1 CU 1+
HELIX 1 1 GLY A 17 GLU A 30 1 14
HELIX 2 2 PRO A 52 THR A 63 1 12
SHEET 1 A 4 LYS A 35 SER A 39 0
SHEET 2 A 4 LEU A 44 THR A 49 -1 O LEU A 44 N SER A 39
SHEET 3 A 4 LYS A 5 VAL A 11 -1 N LYS A 5 O THR A 49
SHEET 4 A 4 VAL A 67 LEU A 73 -1 N ARG A 68 O ASN A 10
LINK CU CU1 A 74 SG CYS A 18 1555 1555 2.12
LINK CU CU1 A 74 SG CYS A 15 1555 1555 2.14
LINK CU CU1 A 74 N CYS A 15 1555 1555 2.75
SITE 1 AC1 4 THR A 14 CYS A 15 CYS A 18 LYS A 65
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
ATOM 1 N MET A 1 -2.865 -21.365 6.547 1.00 0.00 N
ATOM 2 CA MET A 1 -2.324 -21.145 5.197 1.00 0.00 C
ATOM 3 C MET A 1 -2.826 -19.801 4.702 1.00 0.00 C
ATOM 4 O MET A 1 -3.840 -19.328 5.208 1.00 0.00 O
ATOM 5 CB MET A 1 -2.806 -22.207 4.194 1.00 0.00 C
ATOM 6 CG MET A 1 -2.329 -23.622 4.519 1.00 0.00 C
ATOM 7 SD MET A 1 -3.103 -24.357 5.975 1.00 0.00 S
                       .......................................
END
                       .....................................
ATOM 1160 HE22 GLN 72 -11.615 -9.625 -4.828 0.00 0.00 H
ATOM 1161 N LEU 73 -5.839 -9.139 -7.614 0.00 0.00 N
ATOM 1162 CA LEU 73 -5.324 -9.822 -8.785 0.00 0.00 C
ATOM 1163 C LEU 73 -4.703 -11.142 -8.302 0.00 0.00 C
ATOM 1164 OT LEU 73 -4.144 -11.157 -7.174 0.00 0.00 O
ATOM 1165 OT1 LEU 73 -4.752 -12.172 -9.009 0.00 0.00 O1-
ATOM 1166 CB LEU 73 -4.274 -8.950 -9.489 0.00 0.00 C
ATOM 1167 CG LEU 73 -4.872 -7.717 -10.197 0.00 0.00 C
ATOM 1168 CD1 LEU 73 -3.786 -6.668 -10.447 0.00 0.00 C
ATOM 1169 CD2 LEU 73 -5.498 -8.103 -11.541 0.00 0.00 C
ATOM 1170 H LEU 73 -5.263 -9.178 -6.797 0.00 0.00 H
ATOM 1171 HA LEU 73 -6.119 -10.017 -9.505 0.00 0.00 H
ATOM 1172 HB2 LEU 73 -3.556 -8.606 -8.744 0.00 0.00 H
ATOM 1173 HB3 LEU 73 -3.762 -9.560 -10.233 0.00 0.00 H
ATOM 1174 HG LEU 73 -5.643 -7.306 -9.545 0.00 0.00 H
ATOM 1175 HD11 LEU 73 -3.020 -7.087 -11.100 0.00 0.00 H
ATOM 1176 HD12 LEU 73 -3.335 -6.377 -9.498 0.00 0.00 H
ATOM 1177 HD13 LEU 73 -4.229 -5.792 -10.922 0.00 0.00 H
ATOM 1178 HD21 LEU 73 -4.729 -8.514 -12.196 0.00 0.00 H
ATOM 1179 HD22 LEU 73 -5.936 -7.219 -12.006 0.00 0.00 H
ATOM 1180 HD23 LEU 73 -6.275 -8.851 -11.379 0.00 0.00 H
TER 1181 LEU 73
HETATM 1182 CU CU1 74 1.320 12.645 0.576 0.00 0.00 CU2+
CONECT 244 1182
CONECT 272 1182
CONECT 1161 1170 1162
CONECT 1162 1171 1166 1163
CONECT 1163 1165 1164
CONECT 1166 1172 1173 1167
CONECT 1167 1174 1168 1169
CONECT 1168 1175 1176 1177
CONECT 1169 1178 1179 1180
END

And this is the error that spfgen reports:

>Main< (original) 59 % segment L {pdb 1FD8.pdb}
psfgen) building segment L
psfgen) reading residues from pdb file 1FD8.pdb
psfgen) extracted 74 residues from pdb file
psfgen) Info: generating structure...psfgen) Info: skipping improper C-CA-N-HN at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue LEU:73
psfgen) ERROR: Missing atoms for improper CA(0) N(1) C(0) O(0)
    in residue LEU:73
psfgen) Warning: missing atoms for conformation LEU CA-C-N-CA; skipping.
psfgen) Warning: missing atoms for conformation LEU N-CA-C-O; skipping.
psfgen) Warning: missing atoms for conformation LEU N-CA-C-N; skipping.
psfgen) unknown patch type CTER
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

Any help is highly welcomed.

Zoran

Subject: Re: vmd-l: Script to impose coordinates from separate file onto equivalent selection of atoms

Hi Sam,

Well basically you'll need to do it in two steps as you suggested. You'll need to reorder them and make an intermediate pdb file (this isn't strictly needed, but it can be super useful for checking that the order is indeed correct). Next, you can use the "measure fit" command to figure out what the rotation and translation would need to be to minimize the rmsd, and then move it. Suppose you made two atom selections, sel, which would be your intermediate pdb, and ref, which would be your currently modeled linker. Then the following will get your new linker in the vicinity of your old one:

set M [measure fit $sel $ref]
$sel move $M

Now you would just copy the coordinates over:

foreach el [list x y z] {
$ref set $el [$sel get $el]
}

Now it might be, if the linkers have substantially different structure, that this approach won't fit very well. Then my suggestion would be to move the whole linker to match one end, then to move the whole domain to fit the other side of the linker. Be careful that you don't introduce strange structural artifacts (like cis peptides or alternate chiralities) without meaning too, but these can be checked for easily.

-Josh Vermaas

On 3/26/15 6:21 AM, Sam Wallace wrote:

  I'm wondering if anyone has attempted anything similar

  What I'm trying to do is below
  ---

  I have a psf and pdb of a molecule with a small linker joining two larger substituents.

  I have performed some DFT calculations in a different program of the linker only and have geometry output for a few states I'm interested in.

  I would like to read in the output of the DFT calculations and then set the geometry in the pdb file of just the linker component.
  ---

  The approach I'm considering taking
  ---

  The atoms of the linker in the PDB are conveniently id numbers 0 to 24. In the DFT output the atoms aren't in the same order, but I could probably build a map so they correspond correctly, thus any operation that reads from an atom in the DFT output, could write to it's corresponding atom in the PDB.

  Where I'm a bit stuck for ideas is what operation to proceed with after that point. I'm sure I could read the x, y, z coordinates from the DFT and write them to the PDB, but that would result in the linker being displaced from where it should be (to some degree)

  Does anyone have any ideas on how to help?

  Thanks,

  -Sam