Hi Francesco, You can probably send further replies directly to me or Elaine since this is getting pretty detailed and is probably not of much interest to the rest of the list. On Oct 24, 2007, at 2:29 AM, Francesco Pietra wrote:
Hi Eric: I do believe things are now rightly channeled. Though, there are messages that I do not understand. To this concern, which part of the chimera guidelines should be mastered, if not all parts?
I started again (with Chimera 17 Oct daily build) from the non- standard-pdb protein model that you had in large part fixed.
I have now put in further fixes for some of the situations found in your files. You should get the October 24th build and use that (available about 6 hours from now).
I did in this sequence:
(1) Deleting the single HOH molecule still present deep into the pore.
(2) Replacing HIS with HID (as HID was evident from Chimera graphics).
(3) Replacing ASP and GLU with ASH and GLH, respectively. In addition, swapping the names for the oxygens and changing "1" to "2" in the proton name for both ASH and GLH.
Also, some of these residues are carboxylates rather than carboxylic acids. You should leave the carboxylate residue names as ASP/GLU.
(4) Insert "TER" (columns 1-3) to get rid of long bonds.
(5) From command line del:#,#,#,1@H
(6) Running Dock-Prep (all selected, except "Delete non-complexed ions"; also consider H-bonds; residue name HID specified. A query was presented (in SYBYL naming) that I did not find where to get help about; therefore, I accepted the charge settings as it was presented:
ASH + ALA + ASN +0
ASH + ALA + PRO +0
ASH + GLY + MET +0
GLH + ARG + LEU (w/HE2-1) +1
GLH + ARG + LEU (wo/HE2-1) +0
GLH + ARG + THR (w/1H-3) (wo/OXT-3) +1
GLH + ARG + THR (w/OXT-3) (wo/1H-3) +0
Will not happen with the October 24 build. --Eric
On saving mol2, 1 model(s) had non-integral charge. I loaded this mol2 file to Chimera and saved as pdb.
As to the non-integrals, from the log file: The following residues had non-integral charges: ARG 16.X 0.959956 GLH 17.X -0.000762712 LEU 18.X 0.0411068 ALA 39.X 0.0239333 GLH 40.X -0.00136667 ALA 41.X -0.0225667 ASH 42.X -0.0299946 ASN 43.X 0.0290135 PRO 52.X -0.00862973 ASH 53.X -0.0208919 ALA 54.X 0.0297216 GLY 68.X 0.00385946 ASH 69.X -0.0233324 MET 70.X 0.019273 ARG 109.X 0.99236 GLH 110.X 0.03004 THR 111.X -0.0223 ARG 127.X 0.959956 GLH 128.X -0.000762712 LEU 129.X 0.0411068 ALA 150.X 0.0239333 GLH 151.X -0.00136667 ALA 152.X -0.0225667 ASH 153.X -0.0299946 ASN 154.X 0.0290135 PRO 163.X -0.00862973 ASH 164.X -0.0208919 ALA 165.X 0.0297216 GLY 179.X 0.00385946 ASH 180.X -0.0233324 MET 181.X 0.019273 ARG 220.X 0.99236 GLH 221.X 0.03004 THR 222.X -0.0223 ARG 238.X 0.921552 GLH 239.X -0.870055 LEU 240.X -0.0509966 ALA 261.X 0.0239333 GLH 262.X -0.00136667 ALA 263.X -0.0225667 ASH 264.X -0.0299946 ASN 265.X 0.0290135 PRO 274.X -0.00862973 ASH 275.X -0.0208919 ALA 276.X 0.0297216 GLY 290.X 0.00385946 ASH 291.X -0.0233324 MET 292.X 0.019273 ARG 331.X 0.99236 GLH 332.X 0.03004 THR 333.X -0.0223 ARG 349.X 0.921552 GLH 350.X -0.870055 LEU 351.X -0.0509966 ALA 372.X 0.0239333 GLH 373.X -0.00136667 ALA 374.X -0.0225667 ASH 375.X -0.0299946 ASN 376.X 0.0290135 PRO 385.X -0.00862973 ASH 386.X -0.0208919 ALA 387.X 0.0297216 GLY 401.X 0.00385946 ASH 402.X -0.0233324 MET 403.X 0.019273 ARG 442.X 0.990084 GLH 443.X -0.00581091 THR 444.X -0.984373 1 model(s) had non-integral total charge.
I examined on Chimera the THR 444.X. It is terminal, thus OK -1 charge (on OXT carboxylate oxygen). This THR on the saved pbd reads as follows: HETATM 6894 O GLH X 443 -14.087 17.680 23.309 1.00 0.00 O ATOM 6895 N THR X 444 -13.468 15.692 22.402 1.00 0.00 N ATOM 6896 H THR X 444 -12.701 15.104 22.036 1.00 0.00 H ATOM 6897 CA THR X 444 -14.614 14.887 22.695 1.00 0.00 C ATOM 6898 HA THR X 444 -15.533 15.302 22.270 1.00 0.00 H ATOM 6899 CB THR X 444 -14.455 13.483 21.996 1.00 0.00 C ATOM 6900 HB THR X 444 -15.409 12.889 22.079 1.00 0.00 H ATOM 6901 CG2 THR X 444 -14.392 13.621 20.466 1.00 0.00 C ATOM 6902 1HG2 THR X 444 -14.437 12.695 19.945 1.00 0.00 H ATOM 6903 2HG2 THR X 444 -15.193 14.291 20.199 1.00 0.00 H ATOM 6904 3HG2 THR X 444 -13.474 14.106 20.129 1.00 0.00 H ATOM 6905 OG1 THR X 444 -13.355 12.751 22.443 1.00 0.00 O ATOM 6906 HG1 THR X 444 -12.543 13.311 22.233 1.00 0.00 H ATOM 6907 C THR X 444 -14.809 14.814 24.227 1.00 0.00 C ATOM 6908 O THR X 444 -15.798 15.199 24.830 1.00 0.00 O ATOM 6909 OXT THR X 444 -13.895 14.330 24.891 1.00 0.00 O CONECT 255 258 256 236
I did nothing more (planned flex docking and amber_score with DOCK). I'll wait until the above is approved or rejected. (I was unable to command the visualization in Chimera of a particular residue, say THR 444. Command :THR:444 returned all THR.
Thanks
francesco
--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Francesco, As I thought might be the case and mentioned in the previous mail, Amber expects protonated aspartic/glutamic acids to have the proton attached to the other oxygen. What you need to do is simply swap the names of the oxygens in these residues and also change the '1' in the proton name to '2'. You were right to break the long bonds, but breaking the bonds turns the formerly connected residues into terminal residues, which means you need an additional oxygen on the 'C' and two additional hydrogens on the 'N'. In addition the hydrogen already attached to 'N' now has the wrong name, since the three hydrogens connected to an N terminus are named H1, H2, and H3, not H. Probably the simplest way to resolve this situation is to run your structure through Dock Prep again (which will fix up the mangled terminii) and write a new PDB file. Also, you will need to delete the unwanted N-terminal 'H' hydrogens before running Dock Prep. You can either just delete them from your input file or use the command 'del :334,223,112,1@H'.
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Oct 23, 2007, at 10:33 AM, Francesco Pietra wrote:
Thanks to Eric Pettersen I have fixed problems of long bonds and mis-assignement by prepare_amber.pl (from HIS to HIE, while it is HID).
Two types of problems remain because I was either unable to correct or did wrongly. The error log from attempted fixing problems: WARNING: The unperturbed charge of the unit: 24.000000 is not zero. FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 334>.A<H 14> does not have a type. FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 223>.A<H 14> does not have a type. FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 112>.A<H 14> does not have a type. FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 1>.A<H 14> does not have a type.
UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my protein.pdb, the section around residues 333/334:
ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00 0.00 O TER 5156 THR X 333 ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00 0.00 N ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00 0.00 H ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00 0.00 C ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00 0.00 H ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00 0.00 C ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00 0.00 H ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00 0.00 H ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00 0.00 O ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00 0.00 H ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00 0.00 C ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00 0.00 O
Actually, I only inserted "TER" (where it is now) between residue 333 and 334 to get rid of a long bond between the two; numbering and THR X 333 came out automatically. Also, automatically the pdb file now begins with a series of HELIX.
BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section
ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00 ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00 ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00 ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00
was rewritten by exchanging two lines, which automatically were renumbered
ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00 0.00 C ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00 0.00 O ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00 0.00 O ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00 0.00 H ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00 0.00 C
and the issue on prepare_amber.pl was not resolved.
It is obvious that I am carrying out such adjustments for the first time. I got the impression that from now on, what I do increases the mess.
Must say that with my imperfect pdb I could carry outt all DOCK tutorials, except the amber_score.
Thanks francesco pietra
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